FAIRMol

Z64375248

Pose ID 3229 Compound 2243 Pose 519

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 Z64375248
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
16.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.65, Jaccard 0.52, H-bond role recall 0.33
Burial
95%
Hydrophobic fit
67%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.189 kcal/mol/HA) ✓ Good fit quality (FQ -10.14) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Moderate strain (16.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-24.973
kcal/mol
LE
-1.189
kcal/mol/HA
Fit Quality
-10.14
FQ (Leeson)
HAC
21
heavy atoms
MW
304
Da
LogP
3.44
cLogP
Strain ΔE
16.4 kcal/mol
SASA buried
95%
Lipo contact
67% BSA apolar/total
SASA unbound
513 Ų
Apolar buried
326 Ų

Interaction summary

HB 10 HY 20 PI 2 CLASH 6

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 rank3.146Score-24.973
Inter norm-1.353Intra norm0.164
Top1000noExcludedno
Contacts15H-bonds10
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 SER227 TYR194 TYR283 VAL228 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
Jaccard0.52RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

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
529 1.4395319277421879 -1.16206 -18.1621 5 17 0 0.00 0.00 - no Open
535 2.6105772915794776 -1.29956 -24.3281 8 11 0 0.00 0.00 - no Open
519 3.146360943742681 -1.35327 -24.973 10 15 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 -24.973kcal/mol
Ligand efficiency (LE) -1.1892kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.143
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 303.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.44
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 46.68kcal/mol
Minimised FF energy 30.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 512.6Ų
Total solvent-accessible surface area of free ligand
BSA total 487.7Ų
Buried surface area upon binding
BSA apolar 325.5Ų
Hydrophobic contacts buried
BSA polar 162.2Ų
Polar contacts buried
Fraction buried 95.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1502.9Ų
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 1026.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)