FAIRMol

KB_Leish_138

Pose ID 13043 Compound 5256 Pose 164

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand KB_Leish_138
PDB9IFH↗

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 strong SASA done
Strain ΔE
39.3 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 0.00
Burial
57%
Hydrophobic fit
73%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.429 kcal/mol/HA) ✓ Good fit quality (FQ -4.18) ✓ Good H-bonds (5 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Very high strain energy (39.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-13.313
kcal/mol
LE
-0.429
kcal/mol/HA
Fit Quality
-4.18
FQ (Leeson)
HAC
31
heavy atoms
MW
456
Da
LogP
4.12
cLogP
Strain ΔE
39.3 kcal/mol
SASA buried
57%
Lipo contact
73% BSA apolar/total
SASA unbound
705 Ų
Apolar buried
291 Ų

Interaction summary

HB 5 HY 14 PI 3 CLASH 0
Final rank3.259Score-13.313
Inter norm-0.611Intra norm0.181
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 39.3
Residues
ASN402 GLU467 HIS461 LEU399 PHE396 PRO398 PRO462 SER464 THR397 THR463

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:319; 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
A:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
164 3.258867461191277 -0.610644 -13.3133 5 10 6 0.75 0.00 - 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 -13.313kcal/mol
Ligand efficiency (LE) -0.4295kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.184
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 455.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.12
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.72kcal/mol
Minimised FF energy 60.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 704.8Ų
Total solvent-accessible surface area of free ligand
BSA total 400.8Ų
Buried surface area upon binding
BSA apolar 291.2Ų
Hydrophobic contacts buried
BSA polar 109.6Ų
Polar contacts buried
Fraction buried 56.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3141.2Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1501.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)