FAIRMol

Z57805337

Pose ID 9251 Compound 4090 Pose 443

DB SELECTIONDocking 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 Z57805337
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
13.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.00
Burial
63%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.794 kcal/mol/HA) ✓ Good fit quality (FQ -7.31) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (13.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (10)
Score
-20.634
kcal/mol
LE
-0.794
kcal/mol/HA
Fit Quality
-7.31
FQ (Leeson)
HAC
26
heavy atoms
MW
362
Da
LogP
4.75
cLogP
Strain ΔE
13.8 kcal/mol
SASA buried
63%
Lipo contact
81% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
313 Ų

Interaction summary

HB 2 HY 5 PI 0 CLASH 3
Final rank1.179Score-20.634
Inter norm-0.852Intra norm0.059
Top1000noExcludedno
Contacts11H-bonds2
Artifact reasongeometry warning; 10 clashes; 5 protein contact clashes
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 THR241 TYR370 VAL335 VAL336

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

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 overlap7Native recall0.47
Jaccard0.37RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
443 1.1792308914820866 -0.852363 -20.6337 2 11 7 0.47 0.00 - 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 -20.634kcal/mol
Ligand efficiency (LE) -0.7936kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.312
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 362.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.75
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 70.87kcal/mol
Minimised FF energy 57.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 614.1Ų
Total solvent-accessible surface area of free ligand
BSA total 385.9Ų
Buried surface area upon binding
BSA apolar 313.0Ų
Hydrophobic contacts buried
BSA polar 72.8Ų
Polar contacts buried
Fraction buried 62.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2452.0Ų
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 1415.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)