FAIRMol

Z29467492

Pose ID 13316 Compound 5288 Pose 437

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 Z29467492
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
18.7 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.42, H-bond role recall 0.00
Burial
58%
Hydrophobic fit
85%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.586 kcal/mol/HA) ✓ Good fit quality (FQ -5.17) ✓ Good H-bonds (4 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (18.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-13.468
kcal/mol
LE
-0.586
kcal/mol/HA
Fit Quality
-5.17
FQ (Leeson)
HAC
23
heavy atoms
MW
321
Da
LogP
4.20
cLogP
Strain ΔE
18.7 kcal/mol
SASA buried
58%
Lipo contact
85% BSA apolar/total
SASA unbound
560 Ų
Apolar buried
274 Ų

Interaction summary

HB 4 HY 10 PI 1 CLASH 0
Final rank3.954Score-13.468
Inter norm-0.829Intra norm0.243
Top1000noExcludedno
Contacts9H-bonds4
Artifact reasongeometry warning; 9 clashes; 3 protein clashes
Residues
ASN402 LEU399 LYS407 MET400 PHE396 PRO398 PRO462 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 overlap5Native recall0.62
Jaccard0.42RMSD-
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
437 3.95371874636198 -0.828633 -13.4682 4 9 5 0.62 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 -13.468kcal/mol
Ligand efficiency (LE) -0.5856kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.168
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 321.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.20
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 31.23kcal/mol
Minimised FF energy 12.56kcal/mol

SASA & burial

✓ computed
SASA (unbound) 560.5Ų
Total solvent-accessible surface area of free ligand
BSA total 323.2Ų
Buried surface area upon binding
BSA apolar 274.5Ų
Hydrophobic contacts buried
BSA polar 48.8Ų
Polar contacts buried
Fraction buried 57.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2986.2Ų
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 1524.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)