FAIRMol

Z56902329

Pose ID 12537 Compound 1435 Pose 336

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand Z56902329
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
40.9 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.29, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.277 kcal/mol/HA) ✓ Good fit quality (FQ -11.77) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Extreme strain energy (40.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-33.210
kcal/mol
LE
-1.277
kcal/mol/HA
Fit Quality
-11.77
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Strain ΔE
40.9 kcal/mol
SASA buried
81%
Lipo contact
79% BSA apolar/total
SASA unbound
622 Ų
Apolar buried
401 Ų

Interaction summary

HB 7 HY 15 PI 2 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.102Score-33.210
Inter norm-1.267Intra norm-0.010
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 10 clashes; 1 protein contact clash; 3 severe cofactor-context clashes; high strain Δ 40.9
Residues
ARG228 GLY196 GLY197 LEU227 LEU332 LEU334 MET333 NDP800 PHE198 PHE230 SER364 THR374 TYR221

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap9Native recall0.33
Jaccard0.29RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.25

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
C:NDP800

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
336 0.10214502245811838 -1.26749 -33.2096 7 13 9 0.33 0.20 - no Current
398 2.060629453322421 -0.798133 -17.2509 8 11 0 0.00 0.00 - no Open
419 4.090345340807407 -1.05369 -22.2147 10 19 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -33.210kcal/mol
Ligand efficiency (LE) -1.2773kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.768
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.98
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 95.39kcal/mol
Minimised FF energy 54.47kcal/mol

SASA & burial

✓ computed
SASA (unbound) 622.3Ų
Total solvent-accessible surface area of free ligand
BSA total 506.2Ų
Buried surface area upon binding
BSA apolar 400.6Ų
Hydrophobic contacts buried
BSA polar 105.7Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3039.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1535.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)