FAIRMol

Z56950493

Pose ID 3335 Compound 2001 Pose 625

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
T05
L. major PTR1 L. major
Ligand Z56950493
PDB7PXX↗

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
31.0 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.65, Jaccard 0.61, H-bond role recall 0.33
Burial
96%
Hydrophobic fit
80%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.477 kcal/mol/HA) ✓ Good fit quality (FQ -12.36) ✓ Good H-bonds (4 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (31.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.543
kcal/mol
LE
-1.477
kcal/mol/HA
Fit Quality
-12.36
FQ (Leeson)
HAC
20
heavy atoms
MW
283
Da
LogP
3.61
cLogP
Strain ΔE
31.0 kcal/mol
SASA buried
96%
Lipo contact
80% BSA apolar/total
SASA unbound
495 Ų
Apolar buried
378 Ų

Interaction summary

HB 4 HY 22 PI 3 CLASH 0

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.
Final rank1.047Score-29.543
Inter norm-1.415Intra norm-0.063
Top1000noExcludedno
Contacts12H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 31.0
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 SER227 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.61RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
625 1.046686596335111 -1.41456 -29.5432 4 12 11 0.65 0.33 - 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 -29.543kcal/mol
Ligand efficiency (LE) -1.4772kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.361
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 283.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.61
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.36kcal/mol
Minimised FF energy 76.39kcal/mol

SASA & burial

✓ computed
SASA (unbound) 494.6Ų
Total solvent-accessible surface area of free ligand
BSA total 473.4Ų
Buried surface area upon binding
BSA apolar 377.7Ų
Hydrophobic contacts buried
BSA polar 95.7Ų
Polar contacts buried
Fraction buried 95.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1558.1Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1020.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)