FAIRMol

Z1213671382

Pose ID 9297 Compound 3077 Pose 489

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 Z1213671382
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
12.6 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.40, Jaccard 0.27, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
82%
Reason: 7 internal clashes
7 intramolecular clashes 71% of hydrophobic surface is solvent-exposed (12/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.817 kcal/mol/HA) ✓ Good fit quality (FQ -7.21) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (12.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-18.801
kcal/mol
LE
-0.817
kcal/mol/HA
Fit Quality
-7.21
FQ (Leeson)
HAC
23
heavy atoms
MW
308
Da
LogP
3.05
cLogP
Strain ΔE
12.6 kcal/mol
SASA buried
83%
Lipo contact
82% BSA apolar/total
SASA unbound
566 Ų
Apolar buried
385 Ų

Interaction summary

HB 5 HY 2 PI 0 CLASH 0 ⚠ Exposure 70%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (12/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17 Buried (contacted) 5 Exposed 12 LogP 3.05 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank1.412Score-18.801
Inter norm-0.950Intra norm0.133
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 7 clashes; 1 protein clash
Residues
ARG22 ARG342 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 LEU25 LEU382 SER282 THR21 THR285

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 overlap6Native recall0.40
Jaccard0.27RMSD-
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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
489 1.4121139446366726 -0.950285 -18.801 5 13 6 0.40 0.20 - no Current
482 1.4360792874215622 -1.61886 -36.5852 10 13 0 0.00 0.00 - no Open
538 1.9405720166752334 -1.23671 -27.9548 7 13 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -18.801kcal/mol
Ligand efficiency (LE) -0.8174kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 308.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.05
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 44.05kcal/mol
Minimised FF energy 31.47kcal/mol

SASA & burial

✓ computed
SASA (unbound) 566.3Ų
Total solvent-accessible surface area of free ligand
BSA total 469.6Ų
Buried surface area upon binding
BSA apolar 384.6Ų
Hydrophobic contacts buried
BSA polar 85.0Ų
Polar contacts buried
Fraction buried 82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2432.1Ų
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 1375.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)