FAIRMol

Z31287534

Pose ID 13319 Compound 4238 Pose 440

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 Z31287534
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
36.4 kcal/mol
Protein clashes
0
Internal clashes
24
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 0.00
Burial
51%
Hydrophobic fit
84%
Reason: 24 internal clashes
24 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.505 kcal/mol/HA) ✓ Good fit quality (FQ -5.21) ✓ Good burial (51% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (36.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (24)
Score
-19.185
kcal/mol
LE
-0.505
kcal/mol/HA
Fit Quality
-5.21
FQ (Leeson)
HAC
38
heavy atoms
MW
514
Da
LogP
2.85
cLogP
Final rank
5.1607
rank score
Inter norm
-0.501
normalised
Contacts
11
H-bonds 4
Strain ΔE
36.4 kcal/mol
SASA buried
51%
Lipo contact
84% BSA apolar/total
SASA unbound
828 Ų
Apolar buried
357 Ų

Interaction summary

HBD 1 HBA 1 HY 3 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

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.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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
435 4.231508936563396 -0.666109 -24.8637 5 17 0 0.00 0.00 - no Open
440 5.160687580800631 -0.501281 -19.1848 4 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 -19.185kcal/mol
Ligand efficiency (LE) -0.5049kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.205
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 513.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.85
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 156.48kcal/mol
Minimised FF energy 120.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 828.3Ų
Total solvent-accessible surface area of free ligand
BSA total 423.7Ų
Buried surface area upon binding
BSA apolar 356.9Ų
Hydrophobic contacts buried
BSA polar 66.8Ų
Polar contacts buried
Fraction buried 51.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3210.4Ų
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 1542.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)