FAIRMol

Z271078646

Pose ID 3242 Compound 2303 Pose 532

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 Z271078646
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
38.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.48, H-bond role recall 0.17
Burial
93%
Hydrophobic fit
82%
Reason: 1 severe internal clashes
1 severe internal clashes 5 protein-contact clashes 5 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 (-1.006 kcal/mol/HA) ✓ Good fit quality (FQ -9.39) ✓ Good H-bonds (4 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (38.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-27.166
kcal/mol
LE
-1.006
kcal/mol/HA
Fit Quality
-9.39
FQ (Leeson)
HAC
27
heavy atoms
MW
374
Da
LogP
5.27
cLogP
Final rank
4.4081
rank score
Inter norm
-1.131
normalised
Contacts
17
H-bonds 4
Strain ΔE
38.9 kcal/mol
SASA buried
93%
Lipo contact
82% BSA apolar/total
SASA unbound
627 Ų
Apolar buried
479 Ų

Interaction summary

HBA 4 HY 6 PI 5 CLASH 5 Severe 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap11Native recall0.65
Jaccard0.48RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.20

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
532 4.408121609761389 -1.13101 -27.1659 4 17 11 0.65 0.17 - 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 -27.166kcal/mol
Ligand efficiency (LE) -1.0061kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.387
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.27
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 76.75kcal/mol
Minimised FF energy 37.86kcal/mol

SASA & burial

✓ computed
SASA (unbound) 626.7Ų
Total solvent-accessible surface area of free ligand
BSA total 582.5Ų
Buried surface area upon binding
BSA apolar 479.1Ų
Hydrophobic contacts buried
BSA polar 103.4Ų
Polar contacts buried
Fraction buried 92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1681.3Ų
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 1021.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)