FAIRMol

Z57907392

Pose ID 9444 Compound 838 Pose 636

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 Z57907392
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
26.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.20
Burial
73%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.826 kcal/mol/HA) ✓ Good fit quality (FQ -7.79) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (26.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-23.113
kcal/mol
LE
-0.826
kcal/mol/HA
Fit Quality
-7.79
FQ (Leeson)
HAC
28
heavy atoms
MW
395
Da
LogP
3.70
cLogP
Strain ΔE
26.1 kcal/mol
SASA buried
73%
Lipo contact
78% BSA apolar/total
SASA unbound
657 Ų
Apolar buried
371 Ų

Interaction summary

HB 6 HY 5 PI 0 CLASH 3 ⚠ Exposure 47%
⚠️Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 11 Exposed 10 LogP 3.7 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank1.908Score-23.113
Inter norm-0.798Intra norm-0.028
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 6 clashes; 1 protein clash; moderate strain Δ 26.1
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 MET386 PHE383 SER282 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 overlap8Native recall0.53
Jaccard0.40RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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
649 1.6752774076242054 -1.18325 -33.0089 9 20 0 0.00 0.00 - no Open
630 1.809993289240071 -0.911157 -23.6968 3 22 0 0.00 0.00 - no Open
636 1.9076099152982053 -0.797526 -23.1135 6 13 8 0.53 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 -23.113kcal/mol
Ligand efficiency (LE) -0.8255kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.793
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.70
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.10kcal/mol
Minimised FF energy 25.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 657.2Ų
Total solvent-accessible surface area of free ligand
BSA total 479.3Ų
Buried surface area upon binding
BSA apolar 371.4Ų
Hydrophobic contacts buried
BSA polar 107.9Ų
Polar contacts buried
Fraction buried 72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2495.6Ų
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 1385.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)