FAIRMol

Z19652710

Pose ID 2518 Compound 1854 Pose 485

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 Z19652710
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
7.7 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.40
Burial
85%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.7 kcal/mol) ✓ Excellent LE (-1.308 kcal/mol/HA) ✓ Good fit quality (FQ -10.95) ✓ Good H-bonds (3 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-26.158
kcal/mol
LE
-1.308
kcal/mol/HA
Fit Quality
-10.95
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
3.32
cLogP
Strain ΔE
7.7 kcal/mol
SASA buried
85%
Lipo contact
65% BSA apolar/total
SASA unbound
519 Ų
Apolar buried
286 Ų

Interaction summary

HB 3 HY 20 PI 5 CLASH 0

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
No clash · clashes detected for this pose.
Final rank1.804Score-26.158
Inter norm-1.304Intra norm-0.004
Top1000noExcludedno
Contacts11H-bonds3
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR191 TYR194 VAL230 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 strict2Strict recall0.33
HB same residue+role2HB role recall0.40
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
488 0.07748725599830515 -1.09846 -21.111 5 11 0 0.00 0.00 - no Open
517 0.29968302526280177 -1.03568 -19.5522 4 11 0 0.00 0.00 - no Open
485 1.8038394012921375 -1.30437 -26.1579 3 11 11 0.58 0.40 - 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 -26.158kcal/mol
Ligand efficiency (LE) -1.3079kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.945
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 305.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.32
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -14.44kcal/mol
Minimised FF energy -22.15kcal/mol

SASA & burial

✓ computed
SASA (unbound) 518.9Ų
Total solvent-accessible surface area of free ligand
BSA total 439.1Ų
Buried surface area upon binding
BSA apolar 285.9Ų
Hydrophobic contacts buried
BSA polar 153.2Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1489.8Ų
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 1044.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)