FAIRMol

Z55185189

Pose ID 2553 Compound 580 Pose 520

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 Z55185189
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
15.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.50, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.037 kcal/mol/HA) ✓ Good fit quality (FQ -9.29) ✓ Good H-bonds (4 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (15.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-24.880
kcal/mol
LE
-1.037
kcal/mol/HA
Fit Quality
-9.29
FQ (Leeson)
HAC
24
heavy atoms
MW
339
Da
LogP
1.45
cLogP
Strain ΔE
15.3 kcal/mol
SASA buried
76%
Lipo contact
72% BSA apolar/total
SASA unbound
579 Ų
Apolar buried
320 Ų

Interaction summary

HB 4 HY 14 PI 4 CLASH 2
Final rank2.280Score-24.880
Inter norm-1.033Intra norm-0.004
Top1000noExcludedno
Contacts11H-bonds4
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR194 VAL237 ARG287

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

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
Jaccard0.50RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
509 1.6642680146297553 -1.37966 -34.2036 8 14 0 0.00 0.00 - no Open
520 2.2802793832341397 -1.03284 -24.8801 4 11 10 0.53 0.20 - no Current
547 3.4120942633383224 -1.06783 -26.4181 7 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 -24.880kcal/mol
Ligand efficiency (LE) -1.0367kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.291
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 339.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.45
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.81kcal/mol
Minimised FF energy 84.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 578.6Ų
Total solvent-accessible surface area of free ligand
BSA total 441.3Ų
Buried surface area upon binding
BSA apolar 319.9Ų
Hydrophobic contacts buried
BSA polar 121.5Ų
Polar contacts buried
Fraction buried 76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1531.8Ų
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 1033.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)