FAIRMol

Z25044315

Pose ID 2550 Compound 1657 Pose 517

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
T04
L. major PTR1 L. major
Ligand Z25044315
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
10.9 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
2 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.055 kcal/mol/HA) ✓ Good fit quality (FQ -9.45) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (10.9 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (10)
Score
-25.314
kcal/mol
LE
-1.055
kcal/mol/HA
Fit Quality
-9.45
FQ (Leeson)
HAC
24
heavy atoms
MW
385
Da
LogP
4.28
cLogP
Strain ΔE
10.9 kcal/mol
SASA buried
82%
Lipo contact
83% BSA apolar/total
SASA unbound
591 Ų
Apolar buried
402 Ų

Interaction summary

HB 0 HY 24 PI 1 CLASH 4

HB · H-bonds
No hb · h-bonds detected for this pose.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.425Score-25.314
Inter norm-1.023Intra norm-0.032
Top1000noExcludedno
Contacts12H-bonds0
Artifact reasongeometry warning; 10 clashes; 2 protein contact clashes; 2 cofactor-context clashes
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR191 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap12Native recall0.63
Jaccard0.63RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
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
517 0.4246347756871142 -1.02311 -25.3137 0 12 12 0.63 0.00 - no Current
491 1.7835069759055122 -1.19134 -28.1663 3 14 13 0.68 0.40 - no Open
510 2.1310929517662007 -0.786782 -16.2806 5 11 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 -25.314kcal/mol
Ligand efficiency (LE) -1.0547kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.452
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 385.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.28
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 74.12kcal/mol
Minimised FF energy 63.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 590.8Ų
Total solvent-accessible surface area of free ligand
BSA total 486.4Ų
Buried surface area upon binding
BSA apolar 402.3Ų
Hydrophobic contacts buried
BSA polar 84.1Ų
Polar contacts buried
Fraction buried 82.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1637.0Ų
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 1035.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)