FAIRMol

Z18651473

Pose ID 3337 Compound 1632 Pose 627

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 Z18651473
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
26.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.33
Burial
81%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.854 kcal/mol/HA) ✓ Good fit quality (FQ -8.32) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-26.483
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-8.32
FQ (Leeson)
HAC
31
heavy atoms
MW
437
Da
LogP
4.48
cLogP
Strain ΔE
26.7 kcal/mol
SASA buried
81%
Lipo contact
70% BSA apolar/total
SASA unbound
652 Ų
Apolar buried
367 Ų

Interaction summary

HB 6 HY 24 PI 4 CLASH 3
Final rank2.517Score-26.483
Inter norm-0.947Intra norm0.093
Top1000noExcludedno
Contacts14H-bonds6
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; 2 cofactor-context clashes; moderate strain Δ 26.7
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR191 TYR194 VAL230 VAL237 ARG287

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

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 overlap12Native recall0.71
Jaccard0.63RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

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
630 0.2532786233039106 -0.806142 -24.2196 2 13 13 0.76 0.33 - no Open
627 2.517126991976535 -0.947428 -26.4829 6 14 12 0.71 0.33 - no Current
636 3.106264125904273 -0.612697 -16.9428 6 9 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 -26.483kcal/mol
Ligand efficiency (LE) -0.8543kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.323
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.48
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.78kcal/mol
Minimised FF energy 81.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.4Ų
Total solvent-accessible surface area of free ligand
BSA total 526.1Ų
Buried surface area upon binding
BSA apolar 366.9Ų
Hydrophobic contacts buried
BSA polar 159.2Ų
Polar contacts buried
Fraction buried 80.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1640.8Ų
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 1014.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)