The Seven Target Benchmarks#

mockdock includes 7 curated protein–ligand benchmark targets with pre-computed AutoGrid maps and ChEMBL bioactivity calibrations.

Target Overview#

Benchmark

Target ID

PDB ID

Reference Ligand

Calibration [Low, High]

Fragment SMILES

CHK1

CHEMBL4630

2R0U

M54

[-6.44, -11.79]

O=c1[nH]ccc2ccc3ccccc3c12

DPP4

CHEMBL284

2HHA

3TP

[-6.21, -11.23]

Cc1nnc2n1CCN(c1ccccc1)C2

ITK

CHEMBL2959

3QGW

L7A

[-6.55, -11.45]

Nc1ncnc2c1c(C(=O)N)c[nH]2

PEPCK

CHEMBL2911

2GMV

UN8

[-6.12, -10.98]

O=C(O)c1c[nH]c2ccccc12

PptT

CHEMBL5465373

8GKF

D16

[-6.30, -11.50]

CC1=NC(c2c(N1)ccc([*])c2)=O

TTK

CHEMBL3983

3WZJ

O43

[-6.48, -11.62]

Nc1nccc(n1)-c1cccnc1

VEGFR2

CHEMBL279

3VHE

42Q

[-6.70, -12.10]

c1cnc2[nH]ccc2c1

Benchmark System Details#

CHK1 (Checkpoint Kinase 1)#

  • PDB ID: 2R0U

  • Target ID: CHEMBL4630

  • Resolution: 1.70 Å

  • Description: Serine/threonine-protein kinase involved in checkpoint-mediated cell cycle arrest. The benchmark fragment corresponds to a polycyclic lactam core from compound M54.

DPP4 (Dipeptidyl Peptidase IV)#

  • PDB ID: 2HHA

  • Target ID: CHEMBL284

  • Resolution: 2.05 Å

  • Description: Protease target for type 2 diabetes. Uses a piperazine-fused triazole scaffold.

ITK (Interleukin-2 Inducible T-cell Kinase)#

  • PDB ID: 3QGW

  • Target ID: CHEMBL2959

  • Resolution: 2.00 Å

  • Description: Tyrosine kinase key for T-cell signaling. Features an amino-pyrimidine / pyrrolopyrimidine hinge-binding motif.

PEPCK (Phosphoenolpyruvate Carboxykinase)#

  • PDB ID: 2GMV

  • Target ID: CHEMBL2911

  • Resolution: 1.50 Å

  • Description: Key metabolic enzyme in gluconeogenesis. The fragment is an indole-2-carboxylic acid scaffold.

PptT (Phosphopantetheinyl Transferase)#

  • PDB ID: 8GKF

  • Target ID: CHEMBL5465373

  • Resolution: 1.85 Å

  • Description: Essential Mycobacterium tuberculosis enzyme target. Uses a quinazolinone / imidazopyridine derived fragment.

TTK (Dual Specificity Protein Kinase TTK / MPS1)#

  • PDB ID: 3WZJ

  • Target ID: CHEMBL3983

  • Resolution: 2.10 Å

  • Description: Essential mitotic spindle assembly kinase. Features a bipyridine-like motif.

VEGFR2 (Vascular Endothelial Growth Factor Receptor 2)#

  • PDB ID: 3VHE

  • Target ID: CHEMBL279

  • Resolution: 1.55 Å

  • Description: Receptor tyrosine kinase governing angiogenesis. Uses a pyrrolopyridine hinge binder core.

Special Scaffold Notes#

PptT / LibInvent Two-Attachment Scaffold#

For single-exit-vector generative models (e.g. PromptSMILES, REINVENT), PptT uses the single-dummy fragment:

CC1=NC(c2c(N1)ccc([*])c2)=O

However, fragment decorators requiring two attachment points (such as LibInvent) must use the dedicated two-dummy scaffold defined in src/mockdock/configs/PptT.toml:

O=C1N=C([*])Nc2c1cc([*])cc2

Ensure you specify the appropriate scaffold constraint in your model configuration when running multi-attachment benchmarks.