FAIRMol

Z19654250

Pose ID 2611 Compound 1491 Pose 578

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 Z19654250
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
14.7 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.274 kcal/mol/HA) ✓ Good fit quality (FQ -10.66) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (14.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-25.471
kcal/mol
LE
-1.274
kcal/mol/HA
Fit Quality
-10.66
FQ (Leeson)
HAC
20
heavy atoms
MW
321
Da
LogP
3.79
cLogP
Strain ΔE
14.7 kcal/mol
SASA buried
81%
Lipo contact
66% BSA apolar/total
SASA unbound
534 Ų
Apolar buried
286 Ų

Interaction summary

HB 1 HY 13 PI 2 CLASH 2

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-0.727Score-25.471
Inter norm-1.345Intra norm0.072
Top1000noExcludedno
Contacts10H-bonds1
Artifact reasongeometry warning; 5 clashes; 2 cofactor-context clashes
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR191 TYR194 VAL230

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 overlap10Native recall0.53
Jaccard0.53RMSD-
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
578 -0.7270926984500435 -1.34516 -25.4712 1 10 10 0.53 0.20 - no Current
585 1.3723534277399172 -1.28803 -22.9149 4 16 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 -25.471kcal/mol
Ligand efficiency (LE) -1.2736kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.657
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 321.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.79
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -10.82kcal/mol
Minimised FF energy -25.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.1Ų
Total solvent-accessible surface area of free ligand
BSA total 434.3Ų
Buried surface area upon binding
BSA apolar 285.9Ų
Hydrophobic contacts buried
BSA polar 148.3Ų
Polar contacts buried
Fraction buried 81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1510.9Ų
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 1033.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)