FAIRMol

KB_Leish_101

Pose ID 13040 Compound 3637 Pose 161

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_101
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 medium Native strong SASA done
Strain ΔE
33.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.88, H-bond role recall 1.00
Burial
47%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.942 kcal/mol/HA) ✓ Good fit quality (FQ -8.44) ✓ Good H-bonds (5 bonds) ✓ Good burial (47% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (33.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-22.602
kcal/mol
LE
-0.942
kcal/mol/HA
Fit Quality
-8.44
FQ (Leeson)
HAC
24
heavy atoms
MW
341
Da
LogP
2.23
cLogP
Final rank
2.8925
rank score
Inter norm
-0.844
normalised
Contacts
7
H-bonds 5
Strain ΔE
33.4 kcal/mol
SASA buried
47%
Lipo contact
79% BSA apolar/total
SASA unbound
582 Ų
Apolar buried
216 Ų

Interaction summary

HBD 3 HBA 2 HY 2 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

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
Jaccard0.88RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
122 1.4294401613670145 -1.05673 -27.4014 8 13 0 0.00 0.00 - no Open
118 1.6978978953307686 -1.37463 -35.9825 4 16 0 0.00 0.00 - no Open
161 2.8925039998401707 -0.843529 -22.6019 5 7 7 0.88 1.00 - 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 -22.602kcal/mol
Ligand efficiency (LE) -0.9417kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.440
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 341.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.23
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -38.56kcal/mol
Minimised FF energy -72.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 582.4Ų
Total solvent-accessible surface area of free ligand
BSA total 274.3Ų
Buried surface area upon binding
BSA apolar 216.3Ų
Hydrophobic contacts buried
BSA polar 58.0Ų
Polar contacts buried
Fraction buried 47.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3049.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1504.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)