FAIRMol

KB_Leish_92

Pose ID 13039 Compound 308 Pose 160

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand KB_Leish_92
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
55.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Burial
60%
Hydrophobic fit
87%
Reason: strain 55.2 kcal/mol
strain ΔE 55.2 kcal/mol 1 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.755 kcal/mol/HA) ✓ Good fit quality (FQ -7.04) ✓ Strong H-bond network (8 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Extreme strain energy (55.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-20.375
kcal/mol
LE
-0.755
kcal/mol/HA
Fit Quality
-7.04
FQ (Leeson)
HAC
27
heavy atoms
MW
359
Da
LogP
2.13
cLogP
Strain ΔE
55.2 kcal/mol
SASA buried
60%
Lipo contact
87% BSA apolar/total
SASA unbound
633 Ų
Apolar buried
329 Ų

Interaction summary

HB 8 HY 9 PI 1 CLASH 1 ⚠ Exposure 50%
⚠️Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 10 Exposed 10 LogP 2.13 H-bonds 8
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank4.374Score-20.375
Inter norm-0.733Intra norm-0.022
Top1000noExcludedno
Contacts11H-bonds8
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; high strain Δ 55.2
Residues
ASN402 GLU466 GLU467 LEU399 LYS407 LYS410 PHE396 PRO398 PRO462 THR397 THR463

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

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 overlap6Native recall0.75
Jaccard0.46RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
472 0.4377893302794625 -0.950392 -26.2449 0 11 0 0.00 0.00 - no Open
70 0.47106599804211174 -0.932342 -26.3572 0 12 0 0.00 0.00 - no Open
468 0.6892648734294643 -1.20281 -32.8902 7 13 0 0.00 0.00 - no Open
435 1.2154656197774207 -1.20918 -33.9917 9 16 0 0.00 0.00 - no Open
509 1.673956140477069 -1.03134 -29.6551 2 15 0 0.00 0.00 - no Open
519 1.9262872169038363 -0.995405 -29.7653 2 14 0 0.00 0.00 - no Open
494 3.039605889023859 -1.13239 -31.7742 5 15 0 0.00 0.00 - no Open
454 3.2164434138782974 -1.00198 -27.9483 10 16 0 0.00 0.00 - no Open
478 3.3020607865760265 -0.914987 -27.3309 9 15 0 0.00 0.00 - no Open
479 3.505705638707487 -0.714533 -21.8412 6 11 6 0.75 0.00 - no Open
496 3.6376046883594673 -0.802309 -23.1254 6 12 0 0.00 0.00 - no Open
98 3.939670025094264 -0.990476 -27.5314 10 16 0 0.00 0.00 - no Open
160 4.374456075611729 -0.732508 -20.3753 8 11 6 0.75 0.00 - no Current
117 4.576376594729494 -1.06666 -30.2454 6 15 0 0.00 0.00 - no Open
455 6.222747976212252 -1.01947 -28.54 12 16 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 -20.375kcal/mol
Ligand efficiency (LE) -0.7546kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.041
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 359.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.13
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 55.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 160.73kcal/mol
Minimised FF energy 105.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 633.0Ų
Total solvent-accessible surface area of free ligand
BSA total 380.2Ų
Buried surface area upon binding
BSA apolar 329.5Ų
Hydrophobic contacts buried
BSA polar 50.8Ų
Polar contacts buried
Fraction buried 60.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3092.7Ų
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 1514.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)