FAIRMol

Z54323248

Pose ID 2652 Compound 1671 Pose 619

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 Z54323248
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
63.9 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
67%
Reason: strain 63.9 kcal/mol
strain ΔE 63.9 kcal/mol 2 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.787 kcal/mol/HA) ✓ Good fit quality (FQ -7.43) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (63.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (7)
Score
-22.051
kcal/mol
LE
-0.787
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
28
heavy atoms
MW
421
Da
LogP
2.71
cLogP
Strain ΔE
63.9 kcal/mol
SASA buried
80%
Lipo contact
67% BSA apolar/total
SASA unbound
666 Ų
Apolar buried
357 Ų

Interaction summary

HB 5 HY 18 PI 4 CLASH 4
Final rank0.480Score-22.051
Inter norm-0.858Intra norm0.071
Top1000noExcludedno
Contacts12H-bonds5
Artifact reasongeometry warning; 7 clashes; 2 protein contact clashes; 2 cofactor-context clashes; high strain Δ 63.9
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 SER111 TYR194 VAL237 ARG287

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

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 overlap11Native recall0.58
Jaccard0.55RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
619 0.48041461483005266 -0.858102 -22.0509 5 12 11 0.58 0.40 - no Current
602 0.7782551913172737 -1.13541 -27.5699 14 15 0 0.00 0.00 - no Open
639 3.2764256629868695 -1.08077 -27.3404 8 19 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 -22.051kcal/mol
Ligand efficiency (LE) -0.7875kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.435
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 421.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.71
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 63.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 95.46kcal/mol
Minimised FF energy 31.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 666.0Ų
Total solvent-accessible surface area of free ligand
BSA total 532.7Ų
Buried surface area upon binding
BSA apolar 356.7Ų
Hydrophobic contacts buried
BSA polar 176.0Ų
Polar contacts buried
Fraction buried 80.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1565.4Ų
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 1014.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)