FAIRMol

Z45956720

Pose ID 2570 Compound 1664 Pose 537

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 Z45956720
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
26.7 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
90%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.827 kcal/mol/HA) ✓ Good fit quality (FQ -7.29) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (10)
Score
-19.012
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-7.29
FQ (Leeson)
HAC
23
heavy atoms
MW
307
Da
LogP
4.13
cLogP
Strain ΔE
26.7 kcal/mol
SASA buried
80%
Lipo contact
90% BSA apolar/total
SASA unbound
543 Ų
Apolar buried
393 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 2
Final rank0.450Score-19.012
Inter norm-1.041Intra norm0.215
Top1000noExcludedno
Contacts10H-bonds2
Artifact reasongeometry warning; 10 clashes; 2 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 26.7
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR191 TYR194 VAL230

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 overlap10Native recall0.53
Jaccard0.53RMSD-
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
537 0.44976100275760567 -1.04136 -19.0116 2 10 10 0.53 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 -19.012kcal/mol
Ligand efficiency (LE) -0.8266kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.295
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 307.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.13
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.25kcal/mol
Minimised FF energy 77.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 543.4Ų
Total solvent-accessible surface area of free ligand
BSA total 435.9Ų
Buried surface area upon binding
BSA apolar 393.1Ų
Hydrophobic contacts buried
BSA polar 42.9Ų
Polar contacts buried
Fraction buried 80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1653.1Ų
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 1023.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)