FAIRMol

Z1509345389

Pose ID 2648 Compound 1525 Pose 615

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 Z1509345389
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
3.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.40
Burial
93%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (3.9 kcal/mol) ✓ Excellent LE (-1.562 kcal/mol/HA) ✓ Good fit quality (FQ -11.89) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (5)
Score
-25.001
kcal/mol
LE
-1.562
kcal/mol/HA
Fit Quality
-11.89
FQ (Leeson)
HAC
16
heavy atoms
MW
212
Da
LogP
1.31
cLogP
Strain ΔE
3.9 kcal/mol
SASA buried
93%
Lipo contact
74% BSA apolar/total
SASA unbound
395 Ų
Apolar buried
271 Ų

Interaction summary

HB 2 HY 15 PI 3 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-0.412Score-25.001
Inter norm-1.513Intra norm-0.049
Top1000noExcludedno
Contacts10H-bonds2
Artifact reasongeometry warning; 5 clashes; 2 protein contact clashes; 1 severe cofactor-context clash
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 SER111 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 overlap10Native recall0.53
Jaccard0.53RMSD-
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
615 -0.41243237988409504 -1.51338 -25.0006 2 10 10 0.53 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 -25.001kcal/mol
Ligand efficiency (LE) -1.5625kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.894
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 16HA

Physicochemical properties
Molecular weight 212.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.31
Lipinski: ≤ 5
Rotatable bonds 1

Conformational strain (MMFF94s)
Strain energy (ΔE) 3.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 13.68kcal/mol
Minimised FF energy 9.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 395.3Ų
Total solvent-accessible surface area of free ligand
BSA total 367.6Ų
Buried surface area upon binding
BSA apolar 271.4Ų
Hydrophobic contacts buried
BSA polar 96.3Ų
Polar contacts buried
Fraction buried 93.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1450.7Ų
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 1026.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)