FAIRMol

Z56960380

Pose ID 3326 Compound 2137 Pose 616

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
T05
L. major PTR1 L. major
Ligand Z56960380
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
23.7 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.17
Burial
83%
Hydrophobic fit
76%
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 (-1.080 kcal/mol/HA) ✓ Good fit quality (FQ -9.95) ✓ Good H-bonds (4 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-28.076
kcal/mol
LE
-1.080
kcal/mol/HA
Fit Quality
-9.95
FQ (Leeson)
HAC
26
heavy atoms
MW
426
Da
LogP
4.91
cLogP
Strain ΔE
23.7 kcal/mol
SASA buried
83%
Lipo contact
76% BSA apolar/total
SASA unbound
595 Ų
Apolar buried
379 Ų

Interaction summary

HB 4 HY 22 PI 5 CLASH 4

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
Final rank2.137Score-28.076
Inter norm-1.151Intra norm0.072
Top1000noExcludedno
Contacts13H-bonds4
Artifact reasongeometry warning; 10 clashes; 1 protein clash; 3 cofactor-context clashes; moderate strain Δ 23.7
Residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 TYR191 TYR194 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
Jaccard0.58RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.20

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
616 2.137431905191805 -1.15147 -28.0757 4 13 11 0.65 0.17 - no Current
638 2.3406931886139484 -0.951541 -21.6519 9 17 0 0.00 0.00 - no Open
633 4.016867079788199 -1.20647 -27.4228 11 18 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 -28.076kcal/mol
Ligand efficiency (LE) -1.0798kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.949
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 426.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.91
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 172.16kcal/mol
Minimised FF energy 148.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 595.4Ų
Total solvent-accessible surface area of free ligand
BSA total 496.5Ų
Buried surface area upon binding
BSA apolar 379.1Ų
Hydrophobic contacts buried
BSA polar 117.4Ų
Polar contacts buried
Fraction buried 83.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1611.9Ų
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 1045.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)