FAIRMol

Z241957544

Pose ID 9440 Compound 4173 Pose 632

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z241957544
PDB1NJJ↗

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 but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
13.6 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.20
Burial
79%
Hydrophobic fit
86%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.159 kcal/mol/HA) ✓ Good fit quality (FQ -9.29) ✓ Good H-bonds (4 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (13.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-20.871
kcal/mol
LE
-1.159
kcal/mol/HA
Fit Quality
-9.29
FQ (Leeson)
HAC
18
heavy atoms
MW
282
Da
LogP
3.95
cLogP
Strain ΔE
13.6 kcal/mol
SASA buried
79%
Lipo contact
86% BSA apolar/total
SASA unbound
467 Ų
Apolar buried
315 Ų

Interaction summary

HB 4 HY 5 PI 0 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank3.091Score-20.871
Inter norm-1.218Intra norm0.059
Top1000noExcludedno
Contacts11H-bonds4
Artifact reasongeometry warning; 8 clashes; 3 protein clashes
Residues
ALA334 ARG337 ASP243 ASP385 GLU384 LEU339 MET386 PHE383 THR241 VAL335 VAL336

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap6Native recall0.40
Jaccard0.30RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
632 3.0914835539380747 -1.21812 -20.871 4 11 6 0.40 0.20 - 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 -20.871kcal/mol
Ligand efficiency (LE) -1.1595kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.293
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 282.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.95
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 41.54kcal/mol
Minimised FF energy 27.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 466.7Ų
Total solvent-accessible surface area of free ligand
BSA total 367.5Ų
Buried surface area upon binding
BSA apolar 315.2Ų
Hydrophobic contacts buried
BSA polar 52.4Ų
Polar contacts buried
Fraction buried 78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2351.3Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1412.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)