FAIRMol

Z24585638

Pose ID 3379 Compound 1204 Pose 669

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 Z24585638
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
18.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.17
Burial
81%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.924 kcal/mol/HA) ✓ Good fit quality (FQ -8.82) ✓ Good H-bonds (3 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (18.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-26.787
kcal/mol
LE
-0.924
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
29
heavy atoms
MW
428
Da
LogP
5.38
cLogP
Strain ΔE
18.5 kcal/mol
SASA buried
81%
Lipo contact
72% BSA apolar/total
SASA unbound
631 Ų
Apolar buried
367 Ų

Interaction summary

HB 3 HY 24 PI 5 CLASH 1

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 rank2.284Score-26.787
Inter norm-0.974Intra norm0.050
Top1000noExcludedno
Contacts13H-bonds3
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; 2 cofactor-context clashes
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 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
Jaccard0.67RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
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
653 1.3461306924792613 -0.897843 -18.079 4 17 0 0.00 0.00 - no Open
665 1.8748858058976448 -1.05367 -27.3534 3 16 0 0.00 0.00 - no Open
669 2.284235244877461 -0.973642 -26.787 3 13 12 0.71 0.17 - 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 -26.787kcal/mol
Ligand efficiency (LE) -0.9237kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.38
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.67kcal/mol
Minimised FF energy 42.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 631.5Ų
Total solvent-accessible surface area of free ligand
BSA total 510.6Ų
Buried surface area upon binding
BSA apolar 366.5Ų
Hydrophobic contacts buried
BSA polar 144.0Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1613.3Ų
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 1046.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)