FAIRMol

Z26504319

Pose ID 2699 Compound 981 Pose 666

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 Z26504319
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
48.1 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.20
Burial
62%
Hydrophobic fit
85%
Reason: strain 48.1 kcal/mol
strain ΔE 48.1 kcal/mol 4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.564 kcal/mol/HA) ✓ Good fit quality (FQ -5.59) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Extreme strain energy (48.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-18.605
kcal/mol
LE
-0.564
kcal/mol/HA
Fit Quality
-5.59
FQ (Leeson)
HAC
33
heavy atoms
MW
442
Da
LogP
3.76
cLogP
Strain ΔE
48.1 kcal/mol
SASA buried
62%
Lipo contact
85% BSA apolar/total
SASA unbound
756 Ų
Apolar buried
402 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 5

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 rank3.532Score-18.605
Inter norm-0.789Intra norm0.225
Top1000noExcludedno
Contacts13H-bonds2
Artifact reasongeometry warning; 20 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 40.9
Residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 PRO115 TYR114 TYR191 TYR194

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 overlap12Native recall0.63
Jaccard0.60RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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
646 3.0218553428298325 -0.7853 -21.9362 5 19 0 0.00 0.00 - no Open
666 3.531603759863155 -0.788996 -18.6048 2 13 12 0.63 0.20 - no Current
663 4.322667624698714 -0.715887 -20.9598 4 15 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 -18.605kcal/mol
Ligand efficiency (LE) -0.5638kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.594
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 442.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.76
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 48.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.16kcal/mol
Minimised FF energy -11.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 755.8Ų
Total solvent-accessible surface area of free ligand
BSA total 470.1Ų
Buried surface area upon binding
BSA apolar 401.7Ų
Hydrophobic contacts buried
BSA polar 68.5Ų
Polar contacts buried
Fraction buried 62.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1758.2Ų
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 1073.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)