FAIRMol

Z49545335

Pose ID 2450 Compound 1741 Pose 417

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 Z49545335
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
21.5 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.40
Burial
81%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.002 kcal/mol/HA) ✓ Good fit quality (FQ -8.70) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (21.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-22.038
kcal/mol
LE
-1.002
kcal/mol/HA
Fit Quality
-8.70
FQ (Leeson)
HAC
22
heavy atoms
MW
295
Da
LogP
0.29
cLogP
Strain ΔE
21.5 kcal/mol
SASA buried
81%
Lipo contact
75% BSA apolar/total
SASA unbound
537 Ų
Apolar buried
329 Ų

Interaction summary

HB 2 HY 16 PI 4 CLASH 1

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 rank0.949Score-22.038
Inter norm-1.122Intra norm0.121
Top1000noExcludedno
Contacts9H-bonds2
Artifact reasongeometry warning; 6 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 21.5
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR191 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 strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
417 0.9486544671192209 -1.12223 -22.0379 2 9 9 0.47 0.40 - 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 -22.038kcal/mol
Ligand efficiency (LE) -1.0017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.697
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 295.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.29
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.11kcal/mol
Minimised FF energy 82.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 536.8Ų
Total solvent-accessible surface area of free ligand
BSA total 436.9Ų
Buried surface area upon binding
BSA apolar 328.6Ų
Hydrophobic contacts buried
BSA polar 108.3Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1565.2Ų
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 1026.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)