FAIRMol

Z1269163651

Pose ID 2689 Compound 1649 Pose 656

DB fairmolDocking 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 Z1269163651
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 high Native mixed SASA done
Strain ΔE
29.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.40
Burial
95%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-2.143 kcal/mol/HA) ✓ Good fit quality (FQ -15.32) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ High strain energy (29.0 kcal/mol) ✗ Geometry warnings
Score
-30.000
kcal/mol
LE
-2.143
kcal/mol/HA
Fit Quality
-15.32
FQ (Leeson)
HAC
14
heavy atoms
MW
207
Da
LogP
-3.26
cLogP
Strain ΔE
29.0 kcal/mol
SASA buried
95%
Lipo contact
69% BSA apolar/total
SASA unbound
395 Ų
Apolar buried
257 Ų

Interaction summary

HB 7 HY 10 PI 0 CLASH 2

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.371Score-30.000
Inter norm-1.825Intra norm-0.318
Top1000noExcludedno
Contacts9H-bonds7
Artifact reasongeometry warning; 3 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 29.0
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR194

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 overlap9Native recall0.47
Jaccard0.47RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
656 0.37101244232336955 -1.82493 -30.0003 7 9 9 0.47 0.40 - no Current
658 0.9830157296509761 -2.16191 -34.5301 11 11 0 0.00 0.00 - no Open
668 2.1721279981173005 -1.79816 -27.4368 10 13 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 -30.000kcal/mol
Ligand efficiency (LE) -2.1429kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -15.322
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 207.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -3.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 135.08kcal/mol
Minimised FF energy 106.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 395.2Ų
Total solvent-accessible surface area of free ligand
BSA total 374.2Ų
Buried surface area upon binding
BSA apolar 257.1Ų
Hydrophobic contacts buried
BSA polar 117.0Ų
Polar contacts buried
Fraction buried 94.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1427.7Ų
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 1021.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)