FAIRMol

KB_Leish_4

Pose ID 7541 Compound 100 Pose 89

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
T12
T. brucei R5P T. brucei
Ligand KB_Leish_4
PDB6FXS↗

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 mixed SASA done
Strain ΔE
27.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.50, Jaccard 0.44, H-bond role recall 0.30
Burial
58%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.801 kcal/mol/HA) ✓ Good fit quality (FQ -7.81) ✓ Strong H-bond network (10 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (27.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-24.841
kcal/mol
LE
-0.801
kcal/mol/HA
Fit Quality
-7.81
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
27.4 kcal/mol
SASA buried
58%
Lipo contact
67% BSA apolar/total
SASA unbound
708 Ų
Apolar buried
277 Ų

Interaction summary

HB 10 HY 3 PI 3 CLASH 3 ⚠ Exposure 40%
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 12 Exposed 8 LogP 2.78 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.589Score-24.841
Inter norm-0.898Intra norm0.096
Top1000noExcludedno
Contacts10H-bonds10
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 27.4
Residues
ARG140 ARG144 HIS105 HIS141 TYR97 ARG116 ARG46 GLY73 HIS14 ILE15

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap8Native recall0.50
Jaccard0.44RMSD-
HB strict5Strict recall0.42
HB same residue+role3HB role recall0.30
HB same residue3HB residue recall0.30

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
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 5 0.31 0.20 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 15 0.94 0.50 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 5 0.31 0.20 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 0.00 - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 5 0.31 0.20 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 8 0.50 0.30 - no Current
425 4.484716716621432 -0.989791 -28.8598 6 13 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 -24.841kcal/mol
Ligand efficiency (LE) -0.8013kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.807
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 34.16kcal/mol
Minimised FF energy 6.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 708.4Ų
Total solvent-accessible surface area of free ligand
BSA total 412.4Ų
Buried surface area upon binding
BSA apolar 277.3Ų
Hydrophobic contacts buried
BSA polar 135.1Ų
Polar contacts buried
Fraction buried 58.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2152.9Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 776.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)