FAIRMol

Z25106808

Pose ID 2601 Compound 1528 Pose 568

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
T04
L. major PTR1 L. major
Ligand Z25106808
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 strong SASA done
Strain ΔE
17.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.20
Burial
78%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.154 kcal/mol/HA) ✓ Good fit quality (FQ -10.19) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Moderate strain (17.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2)
Score
-26.549
kcal/mol
LE
-1.154
kcal/mol/HA
Fit Quality
-10.19
FQ (Leeson)
HAC
23
heavy atoms
MW
343
Da
LogP
4.23
cLogP
Strain ΔE
17.7 kcal/mol
SASA buried
78%
Lipo contact
67% BSA apolar/total
SASA unbound
589 Ų
Apolar buried
308 Ų

Interaction summary

HB 2 HY 21 PI 4 CLASH 1

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 rank-0.382Score-26.549
Inter norm-1.171Intra norm0.017
Top1000noExcludedno
Contacts11H-bonds2
Artifact reasongeometry warning; 3 clashes; 2 protein contact clashes; 2 cofactor-context clashes
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR194 ARG287

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 overlap11Native recall0.58
Jaccard0.58RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

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
568 -0.38243515158891495 -1.17091 -26.5491 2 11 11 0.58 0.20 - no Current
567 2.550939125820793 -1.19725 -24.1546 6 19 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 -26.549kcal/mol
Ligand efficiency (LE) -1.1543kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 343.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.23
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.80kcal/mol
Minimised FF energy 40.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 589.3Ų
Total solvent-accessible surface area of free ligand
BSA total 460.2Ų
Buried surface area upon binding
BSA apolar 307.7Ų
Hydrophobic contacts buried
BSA polar 152.6Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1576.7Ų
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 1034.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)