FAIRMol

Z56838410

Pose ID 3323 Compound 2071 Pose 613

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 Z56838410
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 medium Native strong SASA done
Strain ΔE
15.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.33
Burial
80%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.952 kcal/mol/HA) ✓ Good fit quality (FQ -8.77) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Moderate strain (15.3 kcal/mol) ✗ Geometry warnings
Score
-24.746
kcal/mol
LE
-0.952
kcal/mol/HA
Fit Quality
-8.77
FQ (Leeson)
HAC
26
heavy atoms
MW
405
Da
LogP
4.07
cLogP
Strain ΔE
15.3 kcal/mol
SASA buried
80%
Lipo contact
63% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
326 Ų

Interaction summary

HB 5 HY 18 PI 2 CLASH 4

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 rank1.651Score-24.746
Inter norm-1.123Intra norm0.171
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 4 clashes; 1 protein clash; 1 cofactor-context clash
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 PRO115 TYR114 TYR191 TYR194 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 overlap12Native recall0.71
Jaccard0.60RMSD-
HB strict1Strict recall0.14
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
613 -0.18740807024469855 -0.988078 -24.4022 1 19 0 0.00 0.00 - no Open
613 1.6514746782569736 -1.12256 -24.7464 5 15 12 0.71 0.33 - no Current
617 1.948115621628624 -0.885262 -21.5725 8 14 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 -24.746kcal/mol
Ligand efficiency (LE) -0.9518kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.769
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 404.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.07
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -13.22kcal/mol
Minimised FF energy -28.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 646.5Ų
Total solvent-accessible surface area of free ligand
BSA total 518.9Ų
Buried surface area upon binding
BSA apolar 326.3Ų
Hydrophobic contacts buried
BSA polar 192.6Ų
Polar contacts buried
Fraction buried 80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1546.7Ų
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 1052.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)