FAIRMol

Z24314037

Pose ID 3138 Compound 2244 Pose 428

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
T05
L. major PTR1 L. major
Ligand Z24314037
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 medium Native strong SASA done
Strain ΔE
14.9 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.50
Burial
79%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.031 kcal/mol/HA) ✓ Good fit quality (FQ -10.05) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (14.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-31.969
kcal/mol
LE
-1.031
kcal/mol/HA
Fit Quality
-10.05
FQ (Leeson)
HAC
31
heavy atoms
MW
440
Da
LogP
2.46
cLogP
Strain ΔE
14.9 kcal/mol
SASA buried
79%
Lipo contact
72% BSA apolar/total
SASA unbound
704 Ų
Apolar buried
403 Ų

Interaction summary

HB 7 HY 18 PI 4 CLASH 5

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
Final rank3.160Score-31.969
Inter norm-1.045Intra norm0.014
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; 4 cofactor-context clashes
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 LYS16 NDP302 PHE113 SER111 SER112 TYR194 VAL230 ARG287

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
Jaccard0.58RMSD-
HB strict2Strict recall0.29
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
488 1.1350204837366145 -0.70632 -22.4599 3 15 0 0.00 0.00 - no Open
464 1.9650560186041406 -0.711854 -22.8777 4 18 0 0.00 0.00 - no Open
428 3.160047468847212 -1.04503 -31.9693 7 13 11 0.65 0.50 - 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 -31.969kcal/mol
Ligand efficiency (LE) -1.0313kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.047
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 440.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.79kcal/mol
Minimised FF energy 40.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 704.4Ų
Total solvent-accessible surface area of free ligand
BSA total 558.2Ų
Buried surface area upon binding
BSA apolar 403.3Ų
Hydrophobic contacts buried
BSA polar 154.9Ų
Polar contacts buried
Fraction buried 79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1685.3Ų
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 1037.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)