FAIRMol

KB_Leish_38

Pose ID 11647 Compound 1260 Pose 126

DB fairmolDocking 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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand KB_Leish_38
PDB6RB5↗

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
27.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.77, Jaccard 0.56
Burial
68%
Hydrophobic fit
94%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.492 kcal/mol/HA) ✓ Good fit quality (FQ -4.84) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (94%) ✗ High strain energy (27.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-15.746
kcal/mol
LE
-0.492
kcal/mol/HA
Fit Quality
-4.84
FQ (Leeson)
HAC
32
heavy atoms
MW
433
Da
LogP
3.36
cLogP
Strain ΔE
27.8 kcal/mol
SASA buried
68%
Lipo contact
94% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
475 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 4

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
Final rank4.630Score-15.746
Inter norm-0.659Intra norm0.167
Top1000noExcludedno
Contacts15H-bonds6
Artifact reasongeometry warning; 20 clashes; 2 protein clashes; moderate strain Δ 27.8
Residues
ASP116 CYS52 GLU18 GLY13 GLY49 ILE339 LEU17 MET113 SER109 SER14 THR335 TRP21 TYR110 VAL53 VAL58

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap10Native recall0.77
Jaccard0.56RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
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:276; 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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
115 1.3601082020539002 -0.848874 -26.1661 6 18 0 0.00 - - no Open
137 2.220095034956826 -0.855068 -20.8737 2 18 0 0.00 - - no Open
126 4.629578488235008 -0.658859 -15.7459 6 15 10 0.77 - - 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 -15.746kcal/mol
Ligand efficiency (LE) -0.4921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.839
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 432.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.36
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 37.09kcal/mol
Minimised FF energy 9.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 741.3Ų
Total solvent-accessible surface area of free ligand
BSA total 503.6Ų
Buried surface area upon binding
BSA apolar 474.9Ų
Hydrophobic contacts buried
BSA polar 28.7Ų
Polar contacts buried
Fraction buried 67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 94.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3326.3Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1460.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)