FAIRMol

Z28636648

Pose ID 2460 Compound 1612 Pose 427

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
T04
L. major PTR1 L. major
Ligand Z28636648
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.42, H-bond role recall 0.20
Burial
66%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.785 kcal/mol/HA) ✓ Good fit quality (FQ -7.13) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (16.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-19.614
kcal/mol
LE
-0.785
kcal/mol/HA
Fit Quality
-7.13
FQ (Leeson)
HAC
25
heavy atoms
MW
346
Da
LogP
5.21
cLogP
Final rank
0.1469
rank score
Inter norm
-0.972
normalised
Contacts
8
H-bonds 1
Strain ΔE
16.0 kcal/mol
SASA buried
66%
Lipo contact
79% BSA apolar/total
SASA unbound
608 Ų
Apolar buried
319 Ų

Interaction summary

HBA 1 HY 3 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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.
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 overlap8Native recall0.42
Jaccard0.42RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
427 0.14689232277911426 -0.971811 -19.6138 1 8 8 0.42 0.20 - 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 -19.614kcal/mol
Ligand efficiency (LE) -0.7846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.132
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 346.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.21
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 11.55kcal/mol
Minimised FF energy -4.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 608.1Ų
Total solvent-accessible surface area of free ligand
BSA total 402.6Ų
Buried surface area upon binding
BSA apolar 319.0Ų
Hydrophobic contacts buried
BSA polar 83.6Ų
Polar contacts buried
Fraction buried 66.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1622.1Ų
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 1073.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)