FAIRMol

KB_Leish_46

Pose ID 13033 Compound 1343 Pose 154

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_46
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
30.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.31, H-bond role recall 1.00
Burial
62%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
2 protein-contact clashes 75% of hydrophobic surface is solvent-exposed (18/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.610 kcal/mol/HA) ✓ Good fit quality (FQ -6.00) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Very high strain energy (30.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-19.525
kcal/mol
LE
-0.610
kcal/mol/HA
Fit Quality
-6.00
FQ (Leeson)
HAC
32
heavy atoms
MW
478
Da
LogP
3.61
cLogP
Strain ΔE
30.0 kcal/mol
SASA buried
62%
Lipo contact
93% BSA apolar/total
SASA unbound
711 Ų
Apolar buried
408 Ų

Interaction summary

HB 2 HY 5 PI 1 CLASH 2 ⚠ Exposure 75%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
75% of hydrophobic surface is solvent-exposed (18/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 24 Buried (contacted) 6 Exposed 18 LogP 3.61 H-bonds 2
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.198Score-19.525
Inter norm-0.587Intra norm-0.023
Top1000noExcludedno
Contacts13H-bonds2
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 30.0
Residues
GLU466 GLU467 GLY459 HIS461 MET400 MET471 PHE396 PRO398 PRO462 SER394 SER464 SER470 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
Jaccard0.31RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
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
140 2.801213136677595 -0.925317 -25.6492 3 14 0 0.00 0.00 - no Open
154 3.198430692215305 -0.587023 -19.525 2 13 5 0.62 1.00 - no Current
92 3.8403208941305516 -1.02026 -28.2546 6 20 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -19.525kcal/mol
Ligand efficiency (LE) -0.6102kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.000
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 478.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.61
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.29kcal/mol
Minimised FF energy 60.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 710.9Ų
Total solvent-accessible surface area of free ligand
BSA total 438.1Ų
Buried surface area upon binding
BSA apolar 408.5Ų
Hydrophobic contacts buried
BSA polar 29.6Ų
Polar contacts buried
Fraction buried 61.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 93.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3211.8Ų
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 1476.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)