FAIRMol

KB_Leish_65

Pose ID 10977 Compound 1142 Pose 134

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand KB_Leish_65
PDB5S9T↗

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 high Native strong SASA done
Strain ΔE
24.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.35, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.501 kcal/mol/HA) ✓ Good fit quality (FQ -5.01) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ High strain energy (24.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-17.021
kcal/mol
LE
-0.501
kcal/mol/HA
Fit Quality
-5.01
FQ (Leeson)
HAC
34
heavy atoms
MW
475
Da
LogP
3.89
cLogP
Strain ΔE
24.0 kcal/mol
SASA buried
82%
Lipo contact
84% BSA apolar/total
SASA unbound
796 Ų
Apolar buried
547 Ų

Interaction summary

HB 6 HY 17 PI 2 CLASH 2
Final rank3.005Score-17.021
Inter norm-0.667Intra norm0.166
Top1000noExcludedno
Contacts19H-bonds6
Artifact reasongeometry warning; 11 clashes; 1 protein clash; moderate strain Δ 24.0
Residues
ARG287 CYS375 GLY197 GLY229 GLY286 GLY376 HIS428 ILE199 ILE378 LEU332 LEU334 LEU377 MET333 PHE198 PHE230 SER364 THR374 VAL362 VAL381

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap8Native recall0.67
Jaccard0.35RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

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
142 1.542018817237739 -0.817819 -24.2304 7 18 0 0.00 0.00 - no Open
119 2.46774917906516 -0.7188 -19.5282 2 17 0 0.00 0.00 - no Open
134 3.004773157258972 -0.666924 -17.0211 6 19 8 0.67 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 -17.021kcal/mol
Ligand efficiency (LE) -0.5006kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.009
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -141.95kcal/mol
Minimised FF energy -165.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 796.2Ų
Total solvent-accessible surface area of free ligand
BSA total 648.5Ų
Buried surface area upon binding
BSA apolar 547.3Ų
Hydrophobic contacts buried
BSA polar 101.2Ų
Polar contacts buried
Fraction buried 81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6658.3Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2092.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)