ASIDSAL CHEM

ASIDSAL CHEM / DOCKING LAB

Choose a target.
Explore the binding site.

Compare binding poses, inspect molecular contacts and save your experiments. Each target has its own preparation settings and recorded reference benchmark.

75Recorded reference benchmarks
Target-specific criteriaSee individual records
CloudSaved notebooks and archives
225Recorded benchmark runs
Dock into one targetChoose a target below, then run one compound or a list.Screen one compound against many targetsUp to 10 targets in a single run. Researcher plan.

Plasmodium falciparum · Wild-type

Antimalarial · Folate pathway

PfDHFR

Reference benchmark passed

Explore the wild-type PfDHFR binding site with pyrimethamine as the reference and NADPH retained in the receptor.

Structure and reference
Structure
3QGT · Chain A
Reference ligand
Pyrimethamine
Cofactor
NADPH (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.654 Å1.022 Å0.742 ÅRecorded max 1.022 Å · criterion ≤ 2.0 Å
Open PfDHFR workspace →

Mus musculus · Wild-type kinase domain

Leukaemia · BCR-ABL kinase

c-Abl

Reference benchmark passed

Investigate poses in the mouse c-Abl kinase domain using the imatinib reference protocol.

Structure and reference
Structure
1IEP · Chain A
Reference ligand
Imatinib
Cofactor
None retained
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.387 Å0.384 Å0.559 ÅRecorded max 0.559 Å · criterion ≤ 2.0 Å
Open c-Abl workspace →

SARS-CoV-2 · Wild-type nsp5

Antiviral · COVID-19 main protease

SARS-CoV-2 Mpro

Reference benchmark passed

Explore non-covalent poses in the SARS-CoV-2 main protease binding site using the recorded quercetin reference protocol.

Structure and reference
Structure
7BQY · Chain A
Reference ligand
Quercetin (non-covalent)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.066 Å0.368 Å0.189 ÅRecorded max 0.368 Å · criterion ≤ 2.0 Å
Open SARS-CoV-2 Mpro workspace →

Homo sapiens · Wild-type

Neurodegeneration · Acetylcholinesterase

hAChE

Reference benchmark passed

Investigate the human acetylcholinesterase binding site with huperzine A as the reference and the recorded Vinardo scoring setup.

Structure and reference
Structure
4EY5 · Chain A
Reference ligand
Huperzine A (crystal)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo0.261 Å0.261 Å0.295 ÅRecorded max 0.295 Å · criterion ≤ 2.0 Å
Open hAChE workspace →

Homo sapiens · Wild-type LBD

Breast cancer · Oestrogen receptor

ERα

Reference benchmark passed

Explore the human estrogen receptor alpha ligand-binding domain with 4-hydroxytamoxifen as the antagonist reference.

Structure and reference
Structure
3ERT · Chain A
Reference ligand
4-Hydroxytamoxifen (OHT)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.268 Å1.258 Å1.297 ÅRecorded max 1.297 Å · criterion ≤ 2.0 Å
Open ERα workspace →

Homo sapiens · Wild-type kinase domain

Inflammation · MAP kinase signalling

p38α MAPK

Reference benchmark passed

Investigate the ATP-binding pocket of human p38 alpha MAP kinase using the SB203580 reference protocol.

Structure and reference
Structure
1A9U · Chain A
Reference ligand
SB203580 (crystal)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.505 Å0.490 Å0.496 ÅRecorded max 0.505 Å · criterion ≤ 2.0 Å
Open p38α MAPK workspace →

HIV-1 (HXB2) · Wild-type-like (Q7K/L33I/L63P)

Antiviral · HIV aspartyl protease

HIV-1 Protease

Reference benchmark passed

Explore the HIV-1 protease binding site using lopinavir as the reference ligand.

Structure and reference
Structure
1MUI · Chains A+B
Reference ligand
Lopinavir (ABT-378)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.133 Å1.109 Å1.075 ÅRecorded max 1.133 Å · criterion ≤ 2.0 Å
Open HIV-1 Protease workspace →

Mus musculus · Wild-type (murine)

Inflammation · Cyclooxygenase-2

COX-2

Reference benchmark passed

Investigate murine COX-2 using the SC-558 reference protocol, with haem and calcium retained in the receptor.

Structure and reference
Structure
6COX · Chain A
Reference ligand
SC-558 (crystal, 26 HA)
Cofactor
Haem + Ca²⁺ (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.453 Å0.501 Å0.528 ÅRecorded max 0.528 Å · criterion ≤ 2.0 Å
Open COX-2 workspace →

Saccharomyces cerevisiae YJM789 · Wild-type (CYP51)

Antifungal · S. cerevisiae CYP51

ScCYP51

Reference benchmark passed

Explore the S. cerevisiae CYP51 model with oteseconazole as the reference. This yeast protocol is distinct from C. albicans CYP51.

Structure and reference
Structure
8VK6 · Chain A
Reference ligand
Oteseconazole (VT-1161)
Cofactor
HEM Fe³⁺ (rigid, essential)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.357 Å2.040 Å2.040 ÅRecorded max 2.040 Å · criterion ≤ 2.5 Å
Open ScCYP51 workspace →

Homo sapiens · Stable engineered construct (ALOX5)

Inflammation · 5-lipoxygenase / leukotrienes

5-Lipoxygenase

Reference benchmark passed

Investigate the stable engineered human 5-lipoxygenase construct with NDGA as the reference and the iron cofactor retained.

Structure and reference
Structure
6N2W · 2.03 Å · stable 5-LOX + NDGA (Gilbert et al. 2020)
Reference ligand
NDGA / nordihydroguaiaretic acid (PDB 30Z)
Cofactor
Non-haem Fe²⁺ (essential, retained rigid)
Reference benchmark details

Chain B, Meeko receptor preparation, Fe²⁺ cofactor appended; ETKDGv3/MMFF94s start, AutoDock Vina 1.2.7

3-run recorded RMSD1.504 Å1.594 Å1.960 ÅRecorded max 1.960 Å · criterion ≤ 2.0 Å
Open 5-Lipoxygenase workspace →

Agaricus bisporus (PPO3 surrogate) · Wild-type PPO3, deoxy form

Melanogenesis · Copper oxidase

Tyrosinase

Reference benchmark passed

Explore the mushroom PPO3 tyrosinase model with tropolone as the reference. This is a surrogate model, not human tyrosinase.

Structure and reference
Structure
2Y9X · Chain A · PPO3 + tropolone (Ismaya et al. 2011)
Reference ligand
Tropolone (CCD 0TR, 9 heavy atoms)
Cofactor
Cu-A / Cu-B binuclear copper centre (rigid)
Reference benchmark details

Chain A, CYS83→ALA patch, Meeko receptor preparation, Cu-A/Cu-B appended; ETKDGv3/MMFF94s start, AutoDock Vina 1.2.7

3-run recorded RMSD1.296 Å0.922 Å1.300 ÅRecorded max 1.300 Å · criterion ≤ 2.0 Å
Open Tyrosinase workspace →

Leishmania major · Wild-type (LmDUTPase)

Antiparasitic · Leishmania DNA replication

LmDUTPase

Reference benchmark passed

Investigate L. major dUTPase using a single-chain model, dUMP reference and retained magnesium. Interpret poses within this preparation, which omits intersubunit contacts.

Structure and reference
Structure
2YAZ · Chain A · 2.4 Å
Reference ligand
dUMP (CCD UMP, 20 HA)
Cofactor
Mg²⁺ (rigid, phosphate coordination)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.866 Å1.071 Å0.653 ÅRecorded max 1.071 Å · criterion ≤ 2.0 Å
Open LmDUTPase workspace →

Mus musculus · Wild-type (murine)

Inflammation · Cyclooxygenase-2 (celecoxib)

COX-2 (celecoxib)

Reference benchmark passed

Investigate murine COX-2 using the co-crystallised celecoxib reference, with haem retained in the receptor.

Structure and reference
Structure
3LN1 · Chain A · 2.40 Å
Reference ligand
Celecoxib (crystal, 26 HA)
Cofactor
Haem (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.511 Å0.480 Å0.457 ÅRecorded max 0.511 Å · criterion ≤ 2.0 Å
Open COX-2 (celecoxib) workspace →

Homo sapiens · V600E kinase domain

Melanoma · MAPK pathway kinase

B-Raf V600E

Reference benchmark passed

Explore the oncogenic B-Raf V600E kinase domain with vemurafenib as the reference. The activation loop is unresolved in this structure.

Structure and reference
Structure
3OG7 · Chain A · 2.45 Å
Reference ligand
Vemurafenib (PLX4032, crystal, 33 HA)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.951 Å0.580 Å0.523 ÅRecorded max 0.951 Å · criterion ≤ 2.0 Å
Open B-Raf V600E workspace →

Mycobacterium tuberculosis · Wild-type enoyl-ACP reductase

Tuberculosis · Mycolic acid biosynthesis

InhA

Reference benchmark passed

Investigate the M. tuberculosis InhA substrate site with a triclosan-class reference and NAD retained in the receptor.

Structure and reference
Structure
4TZK · Chain A · 1.62 Å
Reference ligand
Triclosan-class inhibitor (CCD 641, 23 HA)
Cofactor
NAD (rigid, essential)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.559 Å1.612 Å1.342 ÅRecorded max 1.612 Å · criterion ≤ 2.0 Å
Open InhA workspace →

Homo sapiens · Wild-type catalytic domain (CD26)

Type 2 diabetes · Incretin degradation

DPP-4

Reference benchmark passed

Explore the human DPP-4 S1/S2 pockets with a sitagliptin-class reference and the recorded Vinardo scoring setup.

Structure and reference
Structure
1X70 · Chain A · 2.10 Å
Reference ligand
β-amino acid inhibitor (CCD 715, 28 HA)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo0.503 Å0.878 Å0.696 ÅRecorded max 0.878 Å · criterion ≤ 2.0 Å
Open DPP-4 workspace →

Homo sapiens · Wild-type (AKR1B1)

Diabetic complications · Polyol pathway

Aldose reductase

Reference benchmark passed

Investigate human aldose reductase with the IDD594 reference and NADP⁺ retained. The specificity pocket is open in this ultra-high-resolution structure.

Structure and reference
Structure
1US0 · Chain A · 0.66 Å
Reference ligand
IDD594 (CCD LDT, 24 HA)
Cofactor
NADP⁺ (rigid, essential)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.357 Å0.362 Å0.703 ÅRecorded max 0.703 Å · criterion ≤ 2.0 Å
Open Aldose reductase workspace →

Homo sapiens · Wild-type kinase domain (inactive)

Lung cancer · EGFR signalling

EGFR kinase

Reference benchmark passed

Explore the EGFR ATP site with TAK-285 as the reference. Wild-type inactive conformation; T790M and L858R are not modelled.

Structure and reference
Structure
3POZ · Chain A · 1.50 Å
Reference ligand
TAK-285 (CCD 03P, 38 HA)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.112 Å0.853 Å1.143 ÅRecorded max 1.143 Å · criterion ≤ 2.0 Å
Open EGFR kinase workspace →

Influenza A virus (H5N1) · Group-1 N1 neuraminidase

Influenza · Viral neuraminidase

Neuraminidase N1

Reference benchmark passed

Investigate the influenza N1 active site with oseltamivir as the reference and the recorded Vinardo scoring setup.

Structure and reference
Structure
2HU4 · Chain A · 2.50 Å
Reference ligand
Oseltamivir carboxylate (CCD G39, 20 HA)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo1.453 Å0.305 Å0.781 ÅRecorded max 1.453 Å · criterion ≤ 2.0 Å
Open Neuraminidase N1 workspace →

Homo sapiens · Wild-type human enzyme

Oncology and selectivity control · human folate pathway

Human DHFR

Reference benchmark passed

Dock against the human folate enzyme, the counterpart to PfDHFR, and see both scores rather than one.

Structure and reference
Structure
1S3V · Chain A
Reference ligand
Trimethoxyphenyl quinazoline antifolate (CCD TQD)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo0.334 Å0.315 Å0.890 ÅRecorded max 0.890 Å · criterion ≤ 2.0 Å
Open Human DHFR workspace →

Homo sapiens · N17Q/N455Q/N481Q/N486Q glycosylation mutant

Alzheimer disease · cholinesterase selectivity control

Human BChE

Reference benchmark passed

Explore the butyrylcholinesterase gorge with tacrine as the reference, beside the hAChE protocol.

Structure and reference
Structure
4BDS · Chain A
Reference ligand
Tacrine
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.385 Å0.428 Å0.389 ÅRecorded max 0.428 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 4.8 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open Human BChE workspace →

Escherichia coli K-12 · Wild-type bacterial enzyme

Antibacterial · bacterial folate pathway

E. coli DHFR

Reference benchmark passed

Dock against bacterial dihydrofolate reductase with trimethoprim and NADPH retained in the receptor.

Structure and reference
Structure
6XG5 · Chain A
Reference ligand
Trimethoprim
Cofactor
NDP (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.238 Å0.241 Å0.258 ÅRecorded max 0.258 Å · criterion ≤ 2.0 Å
Open E. coli DHFR workspace →

Trypanosoma brucei brucei · Pteridine reductase subunit

African trypanosomiasis · pteridine salvage

T. brucei PTR1

Reference benchmark passed

Explore the pteridine salvage enzyme of the African trypanosome with NADP retained rigid.

Structure and reference
Structure
2X9N · Chain A
Reference ligand
N2-cyclopropyl triazine-2,4,6-triamine (CCD AX3)
Cofactor
NAP (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo0.950 Å0.573 Å0.914 ÅRecorded max 0.950 Å · criterion ≤ 2.0 Å
Open T. brucei PTR1 workspace →

Severe acute respiratory syndrome coronavirus 2 · Nsp3 papain-like protease domain

Antiviral · SARS-CoV-2 papain-like protease

SARS-CoV-2 PLpro

Reference benchmark passed

Dock in the naphthalene site of the papain-like protease, the non-covalent complement to the Mpro protocol.

Structure and reference
Structure
7JRN · Chain A
Reference ligand
GRL-0617 (CCD TTT)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.507 Å0.478 Å0.570 ÅRecorded max 0.570 Å · criterion ≤ 2.0 Å
Open SARS-CoV-2 PLpro workspace →

Mycobacterium tuberculosis H37Rv · Decaprenylphosphoryl-ribose oxidase

Tuberculosis · arabinogalactan biosynthesis

M. tuberculosis DprE1

Reference benchmark passed

Dock in the DprE1 active site with FAD retained rigid, the non-covalent part of this target class.

Structure and reference
Structure
4KW5 · Chain A
Reference ligand
Benzothiazole carbamate (CCD 1W6)
Cofactor
FAD (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.128 Å1.148 Å1.153 ÅRecorded max 1.153 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 6.5 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open M. tuberculosis DprE1 workspace →

Hepatitis C virus (isolate BK) · Genotype 1b polymerase, palm site

Hepatitis C · NS5B polymerase

HCV NS5B

Reference benchmark passed

Dock in the non-nucleoside palm site of the hepatitis C polymerase.

Structure and reference
Structure
2GIR · Chain A
Reference ligand
Thiophene carboxylate (CCD NN3)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.178 Å1.048 Å1.227 ÅRecorded max 1.227 Å · criterion ≤ 2.0 Å
Open HCV NS5B workspace →

Homo sapiens · Monoamine oxidase B, FAD-bound

Parkinson disease · monoamine oxidase B

Human MAO-B

Reference benchmark passed

Dock in the monoamine oxidase B cavity with FAD retained rigid and safinamide as the reference.

Structure and reference
Structure
2V5Z · Chain A
Reference ligand
Safinamide
Cofactor
FAD (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.597 Å0.469 Å0.447 ÅRecorded max 0.597 Å · criterion ≤ 2.0 Å
Open Human MAO-B workspace →

Homo sapiens · Monoamine oxidase A, FAD-bound

Depression and alkaloid pharmacology · monoamine oxidase A

Human MAO-A

Reference benchmark passed

Explore monoamine oxidase A with the beta-carboline alkaloid harmine, beside the MAO-B protocol.

Structure and reference
Structure
2Z5X · Chain A
Reference ligand
Harmine
Cofactor
FAD (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo1.545 Å1.546 Å1.555 ÅRecorded max 1.555 Å · criterion ≤ 2.0 Å
Open Human MAO-A workspace →

Homo sapiens · Ligand-binding domain, agonist-bound

Type 2 diabetes · PPAR-gamma

PPAR-gamma

Reference benchmark passed

Dock in the PPAR-gamma ligand-binding domain using the rosiglitazone reference protocol.

Structure and reference
Structure
2PRG · Chain A
Reference ligand
Rosiglitazone
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo1.263 Å1.358 Å0.885 ÅRecorded max 1.358 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 3.3 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open PPAR-gamma workspace →

Homo sapiens · Ligand-binding domain, agonist-bound

Prostate cancer · androgen receptor

Androgen receptor

Reference benchmark passed

Explore the androgen receptor ligand-binding domain with its natural hormone as the reference.

Structure and reference
Structure
2AM9 · Chain A
Reference ligand
Testosterone
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.253 Å0.440 Å0.589 ÅRecorded max 0.589 Å · criterion ≤ 2.0 Å
Open Androgen receptor workspace →

Homo sapiens · N-terminal ATP-binding domain

Oncology · Hsp90 chaperone

Hsp90-alpha

Reference benchmark passed

Dock in the Hsp90 N-terminal nucleotide pocket, the site the resorcinol and benzamide inhibitors occupy.

Structure and reference
Structure
2XJX · Chain A
Reference ligand
Onalespib (CCD XJX)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.427 Å1.476 Å1.675 ÅRecorded max 1.675 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 3.3 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open Hsp90-alpha workspace →

Homo sapiens · Catalytic domain

Oncology · PARP1 and synthetic lethality

PARP1

Reference benchmark passed

Explore the PARP1 nicotinamide pocket using the olaparib reference protocol.

Structure and reference
Structure
5DS3 · Chain A
Reference ligand
Olaparib (CCD 09L)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.542 Å1.401 Å1.476 ÅRecorded max 1.542 Å · criterion ≤ 2.0 Å
Open PARP1 workspace →

Homo sapiens · Catalytic heavy chain

Anticoagulation · thrombin

Thrombin

Reference benchmark passed

Dock in the thrombin active site with its S1 and S2 pockets, at 1.67 A resolution.

Structure and reference
Structure
1OYT · Chain H
Reference ligand
Fluorobenzyl pyrrolopyrrole inhibitor (CCD FSN)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.628 Å0.439 Å0.448 ÅRecorded max 1.628 Å · criterion ≤ 2.0 Å
Open Thrombin workspace →

Homo sapiens · Catalytic heavy chain

Anticoagulation · factor Xa

Factor Xa

Reference benchmark passed

Explore the factor Xa S1 and S4 pockets using the rivaroxaban reference protocol.

Structure and reference
Structure
2W26 · Chain A
Reference ligand
Rivaroxaban
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.461 Å1.516 Å1.493 ÅRecorded max 1.516 Å · criterion ≤ 2.0 Å
Open Factor Xa workspace →

Homo sapiens · C-terminal hydrolase domain

Inflammation · soluble epoxide hydrolase

Soluble epoxide hydrolase

Reference benchmark passed

Dock in the soluble epoxide hydrolase catalytic tunnel, a lipid-mediator target.

Structure and reference
Structure
5AKE · Chain A
Reference ligand
Dibenzothiophene sulfone urea (CCD 6N0)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.043 Å0.685 Å0.546 ÅRecorded max 1.043 Å · criterion ≤ 2.0 Å
Open Soluble epoxide hydrolase workspace →

Homo sapiens · Catalytic domain

Type 2 diabetes · PTP1B

PTP1B

Reference benchmark passed

Explore the PTP1B phosphotyrosine pocket, a charged and shallow site that tests the scoring function.

Structure and reference
Structure
2QBS · Chain A
Reference ligand
Thiophene dicarboxylate (CCD 024)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.728 Å0.617 Å0.780 ÅRecorded max 0.780 Å · criterion ≤ 2.0 Å
Open PTP1B workspace →

Homo sapiens · Retinal dehydrogenase 1 subunit

Oncology and alcohol metabolism · ALDH1A1

ALDH1A1

Reference benchmark passed

Explore the ALDH1A1 substrate channel at 1.7 A resolution.

Structure and reference
Structure
5L2M · Chain A
Reference ligand
Trimethylfuranocoumarin inhibitor (CCD 6ZY)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo1.028 Å0.899 Å0.826 ÅRecorded max 1.028 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 9.5 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open ALDH1A1 workspace →

Homo sapiens · Corticosteroid dehydrogenase, NADP-bound

Metabolic syndrome · 11beta-HSD1

11beta-HSD1

Reference benchmark passed

Dock in the 11beta-HSD1 steroid pocket with NADP retained rigid and the glycyrrhetinic acid derivative carbenoxolone as the reference.

Structure and reference
Structure
2BEL · Chain A
Reference ligand
Carbenoxolone
Cofactor
NAP (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.352 Å2.142 Å0.930 ÅRecorded max 2.142 Å · criterion ≤ 2.5 Å
Open 11beta-HSD1 workspace →

Homo sapiens · Kinase domain

Haematological malignancy · PIM1 kinase

PIM1 kinase

Reference benchmark passed

Dock in the PIM1 ATP site, a kinase whose hinge lacks the usual lysine-glutamate pairing.

Structure and reference
Structure
2OBJ · Chain A
Reference ligand
Hydroxyphenyl pyridinecarbonitrile (CCD VRV)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.832 Å0.836 Å0.847 ÅRecorded max 0.847 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 3.7 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open PIM1 kinase workspace →

Homo sapiens · Wild-type human CA II

Glaucoma and diuresis · carbonic anhydrase II

Carbonic anhydrase II

Reference benchmark passed

Dock in the carbonic anhydrase II cone with the catalytic zinc retained and acetazolamide as the reference.

Structure and reference
Structure
3HS4 · Chain A
Reference ligand
Acetazolamide
Cofactor
ZN 301 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo1.392 Å1.389 Å1.324 ÅRecorded max 1.392 Å · criterion ≤ 2.0 Å
Open Carbonic anhydrase II workspace →

Homo sapiens · Collagenase-3 catalytic domain

Osteoarthritis · collagenase-3

MMP-13

Reference benchmark passed

Explore the collagenase-3 active site with both zincs retained, the catalytic one contacted by the reference.

Structure and reference
Structure
456C · Chain A
Reference ligand
Pyrimidine dicarboxamide (CCD CBP)
Cofactor
ZN 272 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.857 Å1.017 Å1.050 ÅRecorded max 1.050 Å · criterion ≤ 2.0 Å
Open MMP-13 workspace →

Homo sapiens · Catalytic domain 2

Oncology and neuropathy · HDAC6 catalytic domain 2

HDAC6

Reference benchmark passed

Dock in the HDAC6 catalytic tunnel with the zinc retained and a hydroxamate natural product as the reference.

Structure and reference
Structure
5EDU · Chain A
Reference ligand
Trichostatin A
Cofactor
ZN 901 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.079 Å1.393 Å1.247 ÅRecorded max 1.393 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 2.3 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open HDAC6 workspace →

Bacillus anthracis · Metalloprotease domain

Anthrax · lethal factor metalloprotease

Anthrax lethal factor

Reference benchmark passed

Explore the anthrax lethal factor substrate groove with the catalytic zinc retained.

Structure and reference
Structure
1YQY · Chain A
Reference ligand
Hydroxamate inhibitor (CCD 915)
Cofactor
ZN 781 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.410 Å0.374 Å0.479 ÅRecorded max 0.479 Å · criterion ≤ 2.0 Å
Open Anthrax lethal factor workspace →

Homo sapiens · Catalytic domain

Erectile dysfunction and pulmonary hypertension · PDE5A

PDE5A

Reference benchmark passed

Dock in the PDE5A catalytic pocket with the zinc and magnesium retained; the reference contacts neither.

Structure and reference
Structure
1UDT · Chain A
Reference ligand
Sildenafil
Cofactor
MG 1002, ZN 1001 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.166 Å0.886 Å0.713 ÅRecorded max 1.166 Å · criterion ≤ 2.0 Å
Open PDE5A workspace →

Homo sapiens · Kinase domain

Oncology · VEGFR2 kinase and angiogenesis

VEGFR2

Reference benchmark passed

Dock in the VEGFR2 ATP site with sorafenib, a type II inhibitor that reaches past the gatekeeper, as the reference.

Structure and reference
Structure
4ASD · Chain A
Reference ligand
Sorafenib (CCD BAX)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.530 Å0.624 Å0.539 ÅRecorded max 0.624 Å · criterion ≤ 2.0 Å
Open VEGFR2 workspace →

Homo sapiens · p110-alpha catalytic subunit

Oncology · PI3K alpha

PI3K alpha

Reference benchmark passed

Dock in the PI3K alpha ATP site with alpelisib, the isoform-selective inhibitor, as the reference.

Structure and reference
Structure
4JPS · Chain A
Reference ligand
Alpelisib (CCD 1LT)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.788 Å0.740 Å0.780 ÅRecorded max 0.788 Å · criterion ≤ 2.0 Å
Open PI3K alpha workspace →

Homo sapiens · Kinase domain

Oncology · anaplastic lymphoma kinase

ALK

Reference benchmark passed

Dock in the anaplastic lymphoma kinase ATP site with crizotinib as the reference.

Structure and reference
Structure
2XP2 · Chain A
Reference ligand
Crizotinib (CCD VGH)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.166 Å0.908 Å1.253 ÅRecorded max 1.253 Å · criterion ≤ 2.0 Å
Open ALK workspace →

Homo sapiens · Kinase domain from the CDK2/cyclin A complex

Oncology · CDK2 and cell cycle control

CDK2

Reference benchmark passed

Dock in the CDK2 ATP site with AZD5438 as the reference; the deposition is the cyclin A complex and chain A alone is modelled.

Structure and reference
Structure
6GUE · Chain A
Reference ligand
AZD5438 (CCD FB8)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.829 Å0.828 Å0.806 ÅRecorded max 0.829 Å · criterion ≤ 2.0 Å
Open CDK2 workspace →

Homo sapiens · Catalytic domain

Oncology and neurodegeneration · sirtuin 2

Sirtuin 2

Reference benchmark passed

Dock in the sirtuin 2 selectivity pocket, the enclosed tunnel beside the acetyl-lysine channel, with SirReal2 as the reference.

Structure and reference
Structure
4RMG · Chain A
Reference ligand
SirReal2 (CCD 3TE)
Cofactor
NAD (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.627 Å0.468 Å0.472 ÅRecorded max 0.627 Å · criterion ≤ 2.0 Å
Open Sirtuin 2 workspace →

Homo sapiens · Full-length allosteric form

Oncology · SHP2 allosteric tunnel, RAS-MAPK signalling

SHP2

Reference benchmark passed

Dock in the SHP2 allosteric tunnel where three domains meet, not the catalytic phosphatase site, with SHP099 as the reference.

Structure and reference
Structure
5EHR · Chain A
Reference ligand
SHP099 (CCD 5OD)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.735 Å0.615 Å0.568 ÅRecorded max 0.735 Å · criterion ≤ 2.0 Å
Open SHP2 workspace →

Homo sapiens · NUDT1 hydrolase

Oncology · MTH1 and oxidised nucleotide sanitation

MTH1

Reference benchmark passed

Dock in the MTH1 nucleotide pocket with TH287 as the reference; read the pose ensemble rather than rank 1 alone.

Structure and reference
Structure
4N1T · Chain A
Reference ligand
TH287 (CCD 2GD)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.361 Å0.311 Å0.367 ÅRecorded max 0.367 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 2.1 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open MTH1 workspace →

Homo sapiens · Aldo-keto reductase 1B10, NADP+ bound

Oncology · AKR1B10, isoform pair for aldose reductase

AKR1B10

Reference benchmark passed

Dock in the AKR1B10 anion site with NADP+ retained and tolrestat as the reference; the isoform pair for aldose reductase.

Structure and reference
Structure
1ZUA · Chain X
Reference ligand
Tolrestat (CCD TOL)
Cofactor
NAP (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.709 Å0.916 Å0.894 ÅRecorded max 0.916 Å · criterion ≤ 2.0 Å
Open AKR1B10 workspace →

Oryctolagus cuniculus · Muscle isoform, inhibitor site

Metabolic disease · glycogen phosphorylase and hepatic glucose output

Glycogen phosphorylase

Reference benchmark passed

Dock at the glycogen phosphorylase inhibitor site with flavopiridol as the reference; the deposition is the rabbit muscle enzyme.

Structure and reference
Structure
1C8K · Chain A
Reference ligand
Flavopiridol (CCD CPB)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.767 Å0.850 Å0.677 ÅRecorded max 0.850 Å · criterion ≤ 2.0 Å
Open Glycogen phosphorylase workspace →

Homo sapiens · N-terminal laminin G domain

Endocrinology · sex hormone binding globulin and steroid transport

SHBG

Reference benchmark passed

Dock in the sex hormone binding globulin steroid pocket with a natural androgen metabolite as the reference.

Structure and reference
Structure
1LHO · Chain A
Reference ligand
5-alpha-androstane-3-beta,17-beta-diol (CCD AOM)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.295 Å0.304 Å0.310 ÅRecorded max 0.310 Å · criterion ≤ 2.0 Å
Open SHBG workspace →

Homo sapiens · Catalytic and NAD domains

Antiviral and methylation · S-adenosylhomocysteine hydrolase

SAH hydrolase

Reference benchmark passed

Dock in the S-adenosylhomocysteine hydrolase substrate site with a carbocyclic adenosine analogue as the reference.

Structure and reference
Structure
1LI4 · Chain A
Reference ligand
Neplanocin A analogue (CCD NOC)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.007 Å1.098 Å0.538 ÅRecorded max 1.098 Å · criterion ≤ 2.0 Å
Open SAH hydrolase workspace →

Rattus norvegicus · Isolated ligand binding core

Neurology · kainate receptor GluK1 ligand binding domain

Kainate receptor GluK1

Reference benchmark passed

Dock in the GluK1 glutamate site with the antagonist (S)-ATPO as the reference; the construct is the isolated binding core of the rat receptor.

Structure and reference
Structure
1VSO · Chain A
Reference ligand
(S)-ATPO (CCD AT1)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.682 Å1.101 Å1.685 ÅRecorded max 1.685 Å · criterion ≤ 2.0 Å
Open Kainate receptor GluK1 workspace →

Ureaplasma parvum · Ureaplasma parvum enzyme

Antibacterial · Ureaplasma thymidine kinase

Thymidine kinase

Reference benchmark passed

Dock in the bacterial thymidine kinase nucleoside site with the natural substrate as the reference.

Structure and reference
Structure
2B8T · Chain A
Reference ligand
Thymidine (CCD THM)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.507 Å0.816 Å0.817 ÅRecorded max 0.817 Å · criterion ≤ 2.0 Å
Open Thymidine kinase workspace →

Homo sapiens · Ligand binding domain

Inflammation · glucocorticoid receptor ligand binding domain

Glucocorticoid receptor

Reference benchmark passed

Dock in the glucocorticoid receptor ligand binding pocket, the expanded form this deposition resolves, with its co-crystal steroid as the reference.

Structure and reference
Structure
3BQD · Chain A
Reference ligand
Deacylcortivazol (CCD DAY)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.625 Å0.540 Å0.551 ÅRecorded max 0.625 Å · criterion ≤ 2.0 Å
Open Glucocorticoid receptor workspace →

Homo sapiens · Full-length reductase

Metabolic disease · steroid 5-beta-reductase AKR1D1

Steroid 5-beta-reductase

Reference benchmark passed

Dock in the AKR1D1 steroid channel with testosterone, its natural substrate, as the reference.

Structure and reference
Structure
3BUR · Chain A
Reference ligand
Testosterone (CCD TES)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.351 Å0.394 Å0.635 ÅRecorded max 0.635 Å · criterion ≤ 2.0 Å
Open Steroid 5-beta-reductase workspace →

Homo sapiens · Kinase domain

Oncology · AKT2 kinase and PI3K signalling

AKT2

Reference benchmark passed

Dock in the AKT2 ATP site with GSK690693 as the reference.

Structure and reference
Structure
3D0E · Chain A
Reference ligand
GSK690693 (CCD G93)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.605 Å0.804 Å0.811 ÅRecorded max 0.811 Å · criterion ≤ 2.0 Å
Open AKT2 workspace →

Homo sapiens · Pancreatic isoform, allosteric site

Metabolic disease · glucokinase and glucose sensing

Glucokinase

Reference benchmark passed

Dock at the glucokinase allosteric activator site, not the glucose pocket, with its co-crystal activator as the reference.

Structure and reference
Structure
3F9M · Chain A
Reference ligand
Glucokinase activator (CCD MRK)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.611 Å1.605 Å1.615 ÅRecorded max 1.615 Å · criterion ≤ 2.0 Å
Open Glucokinase workspace →

HIV-1 M:B_HXB2R · p66 subunit, NNRTI pocket

HIV · reverse transcriptase, non-nucleoside site

HIV-1 reverse transcriptase

Reference benchmark passed

Dock in the non-nucleoside pocket of HIV-1 reverse transcriptase with a pyrimidinedione inhibitor as the reference; the p66 subunit alone is modelled.

Structure and reference
Structure
3LAN · Chain A
Reference ligand
Pyrimidinedione NNRTI (CCD KBT)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.564 Å0.530 Å0.707 ÅRecorded max 0.707 Å · criterion ≤ 2.0 Å
Open HIV-1 reverse transcriptase workspace →

Homo sapiens · Kinase domain

Oncology · EPHA3 receptor tyrosine kinase

EPHA3

Reference benchmark passed

Dock in the EPHA3 ATP site with its co-crystal inhibitor as the reference.

Structure and reference
Structure
4G2F · Chain A
Reference ligand
Compound 7 (CCD C07)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.532 Å0.534 Å0.560 ÅRecorded max 0.560 Å · criterion ≤ 2.0 Å
Open EPHA3 workspace →

Homo sapiens · Pyruvate dehydrogenase kinase 2

Metabolic disease · pyruvate dehydrogenase kinase 2

PDK2

Reference benchmark passed

Dock in the PDK2 inhibitor site with its co-crystal sulfonamide as the reference.

Structure and reference
Structure
4MP7 · Chain A
Reference ligand
Isoindoline benzenesulfonamide (CCD PFT)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.663 Å0.646 Å0.685 ÅRecorded max 0.685 Å · criterion ≤ 2.0 Å
Open PDK2 workspace →

Homo sapiens · Core catalytic domain

Signalling · inositol polyphosphate multikinase

IPMK

Reference benchmark passed

Dock in the inositol polyphosphate multikinase site with diosmetin, a dietary flavone, as the reference.

Structure and reference
Structure
6M8D · Chain A
Reference ligand
Diosmetin (CCD J8D)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.585 Å0.598 Å0.553 ÅRecorded max 0.598 Å · criterion ≤ 2.0 Å
Open IPMK workspace →

Homo sapiens · Thalidomide binding domain

Oncology · cereblon, the ligase substrate receptor used by molecular glues

Cereblon

Reference benchmark passed

Dock in the cereblon tri-tryptophan pocket with lenalidomide as the reference; this is the site molecular glues and degrader ligands occupy.

Structure and reference
Structure
9FJX · Chain B
Reference ligand
S-Lenalidomide (CCD LVY)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.185 Å0.831 Å0.323 ÅRecorded max 0.831 Å · criterion ≤ 2.0 Å
Open Cereblon workspace →

Ovis aries · Cyclooxygenase channel

Inflammation · COX-1, isoform pair for COX-2

COX-1

Reference benchmark passed

Dock in the ovine COX-1 cyclooxygenase channel with ibuprofen as the reference. Scored with Vinardo rather than Vina, which ranks an end-over-end flip of the reference first on one seed of three.

Structure and reference
Structure
1EQG · Chain A
Reference ligand
Ibuprofen (CCD IBP)
Cofactor
HEM (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD · Vinardo0.775 Å0.744 Å0.777 ÅRecorded max 0.777 Å · criterion ≤ 2.0 Å
Open COX-1 workspace →

Homo sapiens · Catalytic domain, aspartyl dyad

Alzheimer disease · beta-secretase

BACE1

Reference benchmark passed

Dock in the beta-secretase active site with an aminothiazine inhibitor of the clinical chemotype as the reference; its amidine engages the ASP32 and ASP228 dyad.

Structure and reference
Structure
6UWP · Chain A
Reference ligand
Aminothiazine inhibitor (CCD QKA)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.577 Å0.664 Å0.732 ÅRecorded max 0.732 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 2.4 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open BACE1 workspace →

Homo sapiens · Secreted phospholipase A2 group IIA

Inflammation · secreted phospholipase A2

sPLA2-IIA

Reference benchmark passed

Dock in the secreted phospholipase A2 channel with the catalytic calcium retained and an indole phosphonate as the reference; the reference phosphonate chelates the ion.

Structure and reference
Structure
1DB4 · Chain A
Reference ligand
Indole phosphonate (CCD 8IN)
Cofactor
CA 198, CA 199 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.761 Å0.640 Å0.717 ÅRecorded max 0.761 Å · criterion ≤ 2.0 Å
Open sPLA2-IIA workspace →

Mycobacterium tuberculosis · M. tuberculosis DHFR, NADPH bound

Antibacterial · M. tuberculosis dihydrofolate reductase

MtDHFR

Reference benchmark passed

Dock in the M. tuberculosis dihydrofolate reductase folate site with NADPH retained and methotrexate as the reference; the counterpart to the human and E. coli enzymes already served.

Structure and reference
Structure
1DF7 · Chain A
Reference ligand
Methotrexate (CCD MTX)
Cofactor
NDP (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.508 Å0.417 Å0.503 ÅRecorded max 0.508 Å · criterion ≤ 2.0 Å
Open MtDHFR workspace →

Homo sapiens · Intestinal maltase-glucoamylase, N-terminal domain

Metabolic disease · intestinal alpha-glucosidase

MGAM

Reference benchmark passed

Dock in the intestinal alpha-glucosidase site with a salacinol-class sulfonium pseudo-sugar as the reference.

Structure and reference
Structure
3L4Y · Chain A
Reference ligand
Sulfonium pseudo-sugar (CCD NR4)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.196 Å1.195 Å1.183 ÅRecorded max 1.196 Å · criterion ≤ 2.0 Å
Open MGAM workspace →

Escherichia coli · E. coli peptide deformylase, nickel form

Antibacterial · peptide deformylase

PDF

Reference benchmark passed

Dock in the bacterial peptide deformylase S1 channel with the catalytic nickel retained and actinonin, the natural-product hydroxamate, as the reference.

Structure and reference
Structure
1G2A · Chain A
Reference ligand
Actinonin (CCD BB2)
Cofactor
NI 1169 (rigid)
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.480 Å1.036 Å1.583 ÅRecorded max 1.583 Å · criterion ≤ 2.0 Å
Open PDF workspace →

Homo sapiens · Kinase domain

Oncology · MET receptor tyrosine kinase

MET

Reference benchmark passed

Dock in the MET kinase ATP site with foretinib, the type II inhibitor, as the reference; read the pose ensemble rather than rank 1 alone.

Structure and reference
Structure
3LQ8 · Chain A
Reference ligand
Foretinib (CCD 88Z)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.534 Å1.012 Å1.455 ÅRecorded max 1.534 Å · criterion ≤ 2.0 ÅThe first-ranked pose for the reference ligand is not its crystal binding mode (up to 11.7 A away); the correct mode is among the returned poses. Read the ensemble, not only rank 1.
Open MET workspace →

Homo sapiens · Kelch domain, Nrf2 binding site

Inflammation · Keap1 Kelch domain, Nrf2 site

Keap1

Reference benchmark passed

Dock in the Keap1 Kelch Nrf2 site, a protein-protein interface rather than an enzyme pocket, with a non-covalent naphthalene bis-sulfonamide as the reference.

Structure and reference
Structure
4XMB · Chain A
Reference ligand
Naphthalene bis-sulfonamide (CCD 41P)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD0.817 Å0.796 Å0.928 ÅRecorded max 0.928 Å · criterion ≤ 2.0 Å
Open Keap1 workspace →

Homo sapiens · N-terminal catalytic domain

Metabolic disease · intestinal sucrase-isomaltase

Sucrase-isomaltase

Reference benchmark passed

Dock in the sucrase-isomaltase N-terminal alpha-glucosidase site against a Salacia-class sulfonium sulfate; the counterpart to MGAM.

Structure and reference
Structure
3LPP · Chain B
Reference ligand
Sulfonium sulfate, C12H24O12S2 (CCD KTL)
Cofactor
None
Reference benchmark details

Interactive experiment workspace

3-run recorded RMSD1.481 Å1.419 Å1.417 ÅRecorded max 1.481 Å · criterion ≤ 2.0 Å
Open Sucrase-isomaltase workspace →

Keep the protocol with the result.

Each target opens an experiment notebook where you can review structures, run investigations, compare poses and save a report. Your record keeps the protocol and preparation details with the results.

Reference pose recovery is assessed separately for each receptor setup. Scores from different targets or protocols should not be treated as a calibrated selectivity comparison. Compute availability is shown inside each protocol.

Read the docking methodology →