FAIRMol

Z31271192

Pose ID 9205 Compound 4257 Pose 397

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 Z31271192
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
37.7 kcal/mol
Protein clashes
13
Internal clashes
13
Native overlap
contact recall 0.47, Jaccard 0.35, H-bond role recall 0.60
Burial
77%
Hydrophobic fit
84%
Reason: 13 protein-contact clashes, 13 internal clashes
13 protein-contact clashes 13 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.728 kcal/mol/HA) ✓ Good fit quality (FQ -6.71) ✓ Good H-bonds (5 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (37.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-18.921
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-6.71
FQ (Leeson)
HAC
26
heavy atoms
MW
347
Da
LogP
0.39
cLogP
Final rank
5.4938
rank score
Inter norm
-0.869
normalised
Contacts
12
H-bonds 8
Strain ΔE
37.7 kcal/mol
SASA buried
77%
Lipo contact
84% BSA apolar/total
SASA unbound
589 Ų
Apolar buried
384 Ų

Interaction summary

HBD 3 HBA 2 HY 4 PI 0 CLASH 13

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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

HY · Hydrophobic contacts

CLASH · Clashes

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
Jaccard0.35RMSD-
HB strict2Strict recall0.33
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
408 4.445240340950495 -0.757698 -20.2038 5 8 0 0.00 0.00 - no Open
397 5.4938084297486 -0.869184 -18.9212 8 12 7 0.47 0.60 - 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 -18.921kcal/mol
Ligand efficiency (LE) -0.7277kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.705
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.39
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 169.94kcal/mol
Minimised FF energy 132.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 589.3Ų
Total solvent-accessible surface area of free ligand
BSA total 455.5Ų
Buried surface area upon binding
BSA apolar 383.6Ų
Hydrophobic contacts buried
BSA polar 71.9Ų
Polar contacts buried
Fraction buried 77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2448.3Ų
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 1390.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)