FAIRMol

KB_chagas_202

Pose ID 11695 Compound 269 Pose 174

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand KB_chagas_202
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
31.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.53
Burial
65%
Hydrophobic fit
90%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.722 kcal/mol/HA) ✓ Good fit quality (FQ -6.73) ✓ Good H-bonds (4 bonds) ✓ Deep burial (65% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Very high strain energy (31.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (11)
Score
-19.484
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
27
heavy atoms
MW
366
Da
LogP
0.92
cLogP
Strain ΔE
31.2 kcal/mol
SASA buried
65%
Lipo contact
90% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
379 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 2
Final rank1.422Score-19.484
Inter norm-0.837Intra norm0.115
Top1000noExcludedno
Contacts10H-bonds4
Artifact reasongeometry warning; 11 clashes; 6 protein contact clashes; high strain Δ 31.2
Residues
ASP116 GLU18 GLY112 ILE339 LEU17 MET113 SER109 SER14 TRP21 TYR110

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

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 overlap8Native recall0.62
Jaccard0.53RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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
174 1.4218651417331085 -0.836875 -19.4836 4 10 8 0.62 - - no Current
186 1.7824810351895748 -0.974766 -21.3766 3 16 0 0.00 - - no Open
189 2.6191014864165867 -0.699903 -17.5012 4 12 0 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 -19.484kcal/mol
Ligand efficiency (LE) -0.7216kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.732
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 366.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.92
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.57kcal/mol
Minimised FF energy 126.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.3Ų
Total solvent-accessible surface area of free ligand
BSA total 418.8Ų
Buried surface area upon binding
BSA apolar 379.1Ų
Hydrophobic contacts buried
BSA polar 39.7Ų
Polar contacts buried
Fraction buried 65.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3190.5Ų
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 1469.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)