FAIRMol

Z44425700

Pose ID 3107 Compound 1752 Pose 397

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 Z44425700
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
25.4 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.50
Burial
88%
Hydrophobic fit
77%
Reason: 8 internal clashes
8 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.054 kcal/mol/HA) ✓ Good fit quality (FQ -9.15) ✓ Good H-bonds (5 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (25.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-23.187
kcal/mol
LE
-1.054
kcal/mol/HA
Fit Quality
-9.15
FQ (Leeson)
HAC
22
heavy atoms
MW
295
Da
LogP
2.21
cLogP
Final rank
2.3420
rank score
Inter norm
-1.279
normalised
Contacts
13
H-bonds 7
Strain ΔE
25.4 kcal/mol
SASA buried
88%
Lipo contact
77% BSA apolar/total
SASA unbound
541 Ų
Apolar buried
366 Ų

Interaction summary

HBA 5 HY 5 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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+role3HB role recall0.50
HB same residue3HB residue recall0.60

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
433 1.0284875701196081 -1.09536 -15.4931 2 13 13 0.76 0.17 - no Open
397 2.341974671452044 -1.27859 -23.1874 7 13 12 0.71 0.50 - no Current
421 3.2450121804855576 -1.08428 -19.1139 4 13 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 -23.187kcal/mol
Ligand efficiency (LE) -1.0540kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.151
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 295.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 110.08kcal/mol
Minimised FF energy 84.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 540.9Ų
Total solvent-accessible surface area of free ligand
BSA total 477.0Ų
Buried surface area upon binding
BSA apolar 366.2Ų
Hydrophobic contacts buried
BSA polar 110.8Ų
Polar contacts buried
Fraction buried 88.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1595.3Ų
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 1012.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)