FAIRMol

KB_chagas_115

Pose ID 13061 Compound 4115 Pose 182

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand KB_chagas_115
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 high Native strong SASA done
Strain ΔE
25.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 0.00
Burial
57%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
2 protein-contact clashes 44% of hydrophobic surface appears solvent-exposed (12/27 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 (-0.456 kcal/mol/HA) ✓ Good fit quality (FQ -4.52) ✓ Strong H-bond network (6 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ High strain energy (25.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-15.042
kcal/mol
LE
-0.456
kcal/mol/HA
Fit Quality
-4.52
FQ (Leeson)
HAC
33
heavy atoms
MW
446
Da
LogP
2.33
cLogP
Strain ΔE
25.2 kcal/mol
SASA buried
57%
Lipo contact
93% BSA apolar/total
SASA unbound
803 Ų
Apolar buried
428 Ų

Interaction summary

HB 6 HY 11 PI 1 CLASH 2 ⚠ Exposure 44%

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
⚠️Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (12/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27 Buried (contacted) 15 Exposed 12 LogP 2.33 H-bonds 6
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.965Score-15.042
Inter norm-0.592Intra norm0.136
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 25.2
Residues
ASN402 CYS469 GLU466 GLU467 GLY459 HIS461 LEU399 PHE396 PRO398 SER470 THR397

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 overlap7Native recall0.88
Jaccard0.58RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
174 1.8806002512686402 -0.667633 -17.8132 7 15 0 0.00 0.00 - no Open
142 3.356493477450131 -0.796668 -22.2568 4 18 0 0.00 0.00 - no Open
182 3.964689923326005 -0.591868 -15.0424 6 11 7 0.88 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 -15.042kcal/mol
Ligand efficiency (LE) -0.4558kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.523
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 445.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.33
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 136.72kcal/mol
Minimised FF energy 111.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 803.1Ų
Total solvent-accessible surface area of free ligand
BSA total 460.6Ų
Buried surface area upon binding
BSA apolar 427.8Ų
Hydrophobic contacts buried
BSA polar 32.8Ų
Polar contacts buried
Fraction buried 57.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3297.8Ų
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 1511.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)