FAIRMol

Z25378902

Pose ID 3378 Compound 2124 Pose 668

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
T05
L. major PTR1 L. major
Ligand Z25378902
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
14.3 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.50, H-bond role recall 0.33
Burial
83%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.291 kcal/mol/HA) ✓ Good fit quality (FQ -11.01) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Moderate strain (14.3 kcal/mol) ✗ Geometry warnings
Score
-27.103
kcal/mol
LE
-1.291
kcal/mol/HA
Fit Quality
-11.01
FQ (Leeson)
HAC
21
heavy atoms
MW
321
Da
LogP
3.25
cLogP
Strain ΔE
14.3 kcal/mol
SASA buried
83%
Lipo contact
64% BSA apolar/total
SASA unbound
555 Ų
Apolar buried
292 Ų

Interaction summary

HB 6 HY 14 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 rank2.016Score-27.103
Inter norm-1.460Intra norm0.169
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 4 clashes; 2 protein clashes; 3 cofactor-context clashes
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 MET183 NDP302 PHE113 SER111 TYR194 TYR283 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.59
Jaccard0.50RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
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
668 2.016200057032117 -1.45996 -27.1032 6 13 10 0.59 0.33 - 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 -27.103kcal/mol
Ligand efficiency (LE) -1.2906kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.009
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 321.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.25
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 22.24kcal/mol
Minimised FF energy 7.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 554.7Ų
Total solvent-accessible surface area of free ligand
BSA total 458.6Ų
Buried surface area upon binding
BSA apolar 292.2Ų
Hydrophobic contacts buried
BSA polar 166.4Ų
Polar contacts buried
Fraction buried 82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1532.4Ų
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 1027.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)