FAIRMol

KB_chagas_188

Pose ID 12332 Compound 1249 Pose 131

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand KB_chagas_188
PDB2WOV↗

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
29.3 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.30, Jaccard 0.19, H-bond role recall 0.00
Burial
95%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.923 kcal/mol/HA) ✓ Good fit quality (FQ -8.99) ✓ Good H-bonds (3 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ High strain energy (29.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-28.611
kcal/mol
LE
-0.923
kcal/mol/HA
Fit Quality
-8.99
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.18
cLogP
Strain ΔE
29.3 kcal/mol
SASA buried
95%
Lipo contact
89% BSA apolar/total
SASA unbound
734 Ų
Apolar buried
623 Ų

Interaction summary

HB 3 HY 24 PI 1 CLASH 3

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 rank2.853Score-28.611
Inter norm-1.006Intra norm0.076
Top1000noExcludedno
Contacts23H-bonds3
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; 1 cofactor-context clash; moderate strain Δ 29.0
Residues
ALA363 ALA365 ARG287 ASP327 CYS52 CYS57 GLY56 ILE199 ILE438 LEU334 LYS60 MET333 NDP800 PHE182 PHE203 PHE367 PRO336 PRO435 SER178 SER364 THR335 THR51 VAL55

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap8Native recall0.30
Jaccard0.19RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

493 residues
Protein targetT19Atoms7541
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:330; 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
C:NDP800

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
179 0.498057896689636 -1.07869 -33.2552 5 16 0 0.00 0.00 - no Open
170 2.1614606970409747 -0.892015 -25.1118 3 15 0 0.00 0.00 - no Open
131 2.853103761403765 -1.00634 -28.6112 3 23 8 0.30 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 -28.611kcal/mol
Ligand efficiency (LE) -0.9229kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.992
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.18
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 35.49kcal/mol
Minimised FF energy 6.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 734.4Ų
Total solvent-accessible surface area of free ligand
BSA total 698.5Ų
Buried surface area upon binding
BSA apolar 622.8Ų
Hydrophobic contacts buried
BSA polar 75.7Ų
Polar contacts buried
Fraction buried 95.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3235.8Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1479.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)