FAIRMol

Z31545384

Pose ID 12714 Compound 1315 Pose 513

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 Z31545384
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
41.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.101 kcal/mol/HA) ✓ Good fit quality (FQ -10.93) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Extreme strain energy (41.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-36.350
kcal/mol
LE
-1.101
kcal/mol/HA
Fit Quality
-10.93
FQ (Leeson)
HAC
33
heavy atoms
MW
518
Da
LogP
0.98
cLogP
Strain ΔE
41.1 kcal/mol
SASA buried
89%
Lipo contact
69% BSA apolar/total
SASA unbound
801 Ų
Apolar buried
494 Ų

Interaction summary

HB 7 HY 24 PI 0 CLASH 1
Final rank2.883Score-36.350
Inter norm-0.975Intra norm-0.127
Top1000noExcludedno
Contacts22H-bonds7
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 41.1
Residues
ALA363 ALA365 ARG287 CYS57 GLY56 ILE199 LEU334 LYS60 LYS61 NDP800 PHE182 PHE203 PHE367 PRO336 SER178 SER364 THR335 THR51 VAL337 VAL362 VAL55 VAL58

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

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 overlap7Native recall0.26
Jaccard0.17RMSD-
HB strict2Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue1HB residue recall0.25

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
541 2.617274720249237 -0.87813 -24.2845 6 19 0 0.00 0.00 - no Open
522 2.8162579184003977 -0.830865 -24.6714 4 15 0 0.00 0.00 - no Open
513 2.883076203678775 -0.974716 -36.3498 7 22 7 0.26 0.40 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -36.350kcal/mol
Ligand efficiency (LE) -1.1015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.929
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 517.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.98
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 45.52kcal/mol
Minimised FF energy 4.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 801.4Ų
Total solvent-accessible surface area of free ligand
BSA total 713.4Ų
Buried surface area upon binding
BSA apolar 494.3Ų
Hydrophobic contacts buried
BSA polar 219.1Ų
Polar contacts buried
Fraction buried 89.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3166.4Ų
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 1474.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)