FAIRMol

1NJJ

Pose ID 9486 Compound 4259

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 1NJJ
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding weak Geometry low Native strong SASA done
Strain ΔE
101.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Burial
64%
Hydrophobic fit
87%
Reason: strain 101.3 kcal/mol
strain ΔE 101.3 kcal/mol 1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Strong H-bond network (7 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Extreme strain energy (101.3 kcal/mol)
HAC
34
heavy atoms
MW
501
Da
LogP
-8.79
cLogP
Strain ΔE
101.3 kcal/mol
SASA buried
64%
Lipo contact
87% BSA apolar/total
SASA unbound
757 Ų
Apolar buried
419 Ų

Interaction summary

HB 7 HY 6 PI 0 CLASH 1 ⚠ Exposure 35%
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 13 Exposed 7 LogP -8.79 H-bonds 7
Exposed fragments: cyclohexyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank-Score-
Inter norm-Intra norm-
Top1000noExcludedno
Contacts15H-bonds7
Artifact reasonNative reference ligand
Residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241

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 overlap15Native recall1.00
Jaccard1.00RMSD0.00 Å
HB strict6Strict recall1.00
HB same residue+role5HB role recall1.00
HB same residue5HB residue recall1.00

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
- ★ Native - - - 7 15 15 1.00 1.00 0.00 Å no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Heavy atom count 34HA

Physicochemical properties
Molecular weight 500.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) -8.79
Lipinski: ≤ 5
Rotatable bonds 15

Conformational strain (MMFF94s)
Strain energy (ΔE) 101.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 591.75kcal/mol
Minimised FF energy 490.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 757.1Ų
Total solvent-accessible surface area of free ligand
BSA total 481.5Ų
Buried surface area upon binding
BSA apolar 419.1Ų
Hydrophobic contacts buried
BSA polar 62.3Ų
Polar contacts buried
Fraction buried 63.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2650.7Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1343.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)