FAIRMol

Z15584023

Pose ID 3130 Compound 2196 Pose 420

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 Z15584023
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
27.3 kcal/mol
Protein clashes
4
Internal clashes
6
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.67
Burial
74%
Hydrophobic fit
72%
Reason: 6 internal clashes
4 protein-contact clashes 6 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.911 kcal/mol/HA) ✓ Good fit quality (FQ -8.88) ✓ Good H-bonds (4 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-28.255
kcal/mol
LE
-0.911
kcal/mol/HA
Fit Quality
-8.88
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
5.23
cLogP
Final rank
2.7098
rank score
Inter norm
-0.918
normalised
Contacts
13
H-bonds 7
Strain ΔE
27.3 kcal/mol
SASA buried
74%
Lipo contact
72% BSA apolar/total
SASA unbound
674 Ų
Apolar buried
359 Ų

Interaction summary

HBD 2 HBA 2 HY 4 PI 3 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

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 overlap12Native recall0.71
Jaccard0.67RMSD-
HB strict3Strict recall0.43
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.80

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
523 2.657087346169004 -0.746016 -20.7685 2 13 0 0.00 0.00 - no Open
420 2.709827116277981 -0.918181 -28.2554 7 13 12 0.71 0.67 - no Current
465 2.9022096103635304 -0.838033 -26.0762 4 20 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 -28.255kcal/mol
Ligand efficiency (LE) -0.9115kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.880
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 462.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.23
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -9.32kcal/mol
Minimised FF energy -36.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 674.3Ų
Total solvent-accessible surface area of free ligand
BSA total 496.3Ų
Buried surface area upon binding
BSA apolar 359.2Ų
Hydrophobic contacts buried
BSA polar 137.1Ų
Polar contacts buried
Fraction buried 73.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1557.5Ų
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 1155.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)