FAIRMol

ulfkktlib_1655

Pose ID 13118 Compound 1362 Pose 239

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 ulfkktlib_1655
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
0
Internal clashes
19
Native overlap
contact recall 1.00, Jaccard 0.62, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
89%
Reason: 19 internal clashes
19 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.550 kcal/mol/HA) ✓ Good fit quality (FQ -5.51) ✓ Good H-bonds (3 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (18.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-18.713
kcal/mol
LE
-0.550
kcal/mol/HA
Fit Quality
-5.51
FQ (Leeson)
HAC
34
heavy atoms
MW
450
Da
LogP
3.99
cLogP
Strain ΔE
18.6 kcal/mol
SASA buried
56%
Lipo contact
89% BSA apolar/total
SASA unbound
731 Ų
Apolar buried
368 Ų

Interaction summary

HB 3 HY 21 PI 1 CLASH 0
Final rank4.224Score-18.713
Inter norm-0.558Intra norm0.007
Top1000noExcludedno
Contacts13H-bonds3
Artifact reasongeometry warning; 19 clashes; 2 protein clashes
Residues
ASN402 GLU466 GLU467 LEU399 LYS410 PHE396 PRO398 PRO462 SER394 SER395 SER470 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 overlap8Native recall1.00
Jaccard0.62RMSD-
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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
327 2.825584725469129 -0.741713 -21.4404 3 13 0 0.00 0.00 - no Open
240 3.0132207613293107 -0.813775 -23.0641 4 11 0 0.00 0.00 - no Open
239 4.224087294080507 -0.557673 -18.7127 3 13 8 1.00 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 -18.713kcal/mol
Ligand efficiency (LE) -0.5504kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.507
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.99
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.35kcal/mol
Minimised FF energy 7.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 731.0Ų
Total solvent-accessible surface area of free ligand
BSA total 412.2Ų
Buried surface area upon binding
BSA apolar 367.6Ų
Hydrophobic contacts buried
BSA polar 44.6Ų
Polar contacts buried
Fraction buried 56.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3180.5Ų
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 1537.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)