FAIRMol

Z32301499

Pose ID 12599 Compound 4079 Pose 398

DB fairmolDocking 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 Z32301499
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
23.4 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.33, Jaccard 0.22, H-bond role recall 0.40
Burial
94%
Hydrophobic fit
88%
Reason: 8 internal clashes
8 protein-contact clashes 8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.953 kcal/mol/HA) ✓ Good fit quality (FQ -9.46) ✓ Good H-bonds (5 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ High strain energy (23.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-31.452
kcal/mol
LE
-0.953
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
33
heavy atoms
MW
488
Da
LogP
5.52
cLogP
Strain ΔE
23.4 kcal/mol
SASA buried
94%
Lipo contact
88% BSA apolar/total
SASA unbound
735 Ų
Apolar buried
603 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 8

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 rank3.766Score-31.452
Inter norm-0.998Intra norm0.044
Top1000noExcludedno
Contacts23H-bonds5
Artifact reasongeometry warning; 17 clashes; 1 protein clash; 2 cofactor-context clashes; moderate strain Δ 23.4
Residues
ALA363 ALA365 ARG287 ASP327 CYS57 GLU202 GLY56 ILE199 ILE438 LEU334 LYS60 MET333 NDP800 PHE182 PHE203 PHE367 PRO435 SER162 SER178 SER364 THR335 THR51 VAL55

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
Jaccard0.22RMSD-
HB strict2Strict recall0.17
HB same residue+role2HB role recall0.40
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
398 3.765973798591196 -0.997636 -31.4521 5 23 9 0.33 0.40 - no Current
437 4.412114066828967 -1.00151 -29.8533 8 23 0 0.00 0.00 - no Open
418 6.336929737625268 -0.868344 -21.7276 8 18 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 -31.452kcal/mol
Ligand efficiency (LE) -0.9531kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.456
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 488.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.52
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 63.73kcal/mol
Minimised FF energy 40.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 734.9Ų
Total solvent-accessible surface area of free ligand
BSA total 688.8Ų
Buried surface area upon binding
BSA apolar 603.4Ų
Hydrophobic contacts buried
BSA polar 85.3Ų
Polar contacts buried
Fraction buried 93.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3216.3Ų
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 1482.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)