FAIRMol

KB_HAT_155

Pose ID 13015 Compound 5276 Pose 136

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_HAT_155
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.706 kcal/mol/HA) ✓ Good fit quality (FQ -6.42) ✓ Good H-bonds (5 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (24.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-17.658
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-6.42
FQ (Leeson)
HAC
25
heavy atoms
MW
353
Da
LogP
3.41
cLogP
Strain ΔE
24.4 kcal/mol
SASA buried
56%
Lipo contact
81% BSA apolar/total
SASA unbound
623 Ų
Apolar buried
284 Ų

Interaction summary

HB 5 HY 16 PI 1 CLASH 3
Final rank3.810Score-17.658
Inter norm-0.747Intra norm0.040
Top1000noExcludedno
Contacts9H-bonds5
Artifact reasongeometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 24.4
Residues
ASN402 GLU467 LEU399 LYS410 PHE396 PRO398 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
Jaccard0.55RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
136 3.8104182797945025 -0.746593 -17.6577 5 9 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 -17.658kcal/mol
Ligand efficiency (LE) -0.7063kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.421
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.41
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 42.06kcal/mol
Minimised FF energy 17.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 622.7Ų
Total solvent-accessible surface area of free ligand
BSA total 351.8Ų
Buried surface area upon binding
BSA apolar 284.2Ų
Hydrophobic contacts buried
BSA polar 67.5Ų
Polar contacts buried
Fraction buried 56.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3032.1Ų
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 1525.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)