FAIRMol

Z46033738

Pose ID 9302 Compound 3569 Pose 494

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 Z46033738
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 and worth follow-up
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
10.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.33, H-bond role recall 0.20
Burial
79%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 63% of hydrophobic surface is solvent-exposed (12/19 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 (-0.983 kcal/mol/HA) ✓ Good fit quality (FQ -8.54) ✓ Good H-bonds (5 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (10.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-21.636
kcal/mol
LE
-0.983
kcal/mol/HA
Fit Quality
-8.54
FQ (Leeson)
HAC
22
heavy atoms
MW
292
Da
LogP
3.93
cLogP
Strain ΔE
10.3 kcal/mol
SASA buried
79%
Lipo contact
81% BSA apolar/total
SASA unbound
549 Ų
Apolar buried
351 Ų

Interaction summary

HB 5 HY 9 PI 0 CLASH 3 ⚠ Exposure 63%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
63% of hydrophobic surface is solvent-exposed (12/19 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 19 Buried (contacted) 7 Exposed 12 LogP 3.93 H-bonds 5
Exposed fragments: phenyl (5/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.843Score-21.636
Inter norm-1.072Intra norm0.089
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 8 clashes; 2 protein clashes
Residues
ALA281 ARG22 ASP385 CYS26 GLN341 GLU384 LEU25 LEU382 MET386 PHE284 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 overlap7Native recall0.47
Jaccard0.33RMSD-
HB strict0Strict recall0.00
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
507 1.8526976254695369 -1.09518 -26.1311 6 15 0 0.00 0.00 - no Open
494 2.842978656725251 -1.07242 -21.6358 5 13 7 0.47 0.20 - no Current
481 5.023362851115445 -1.08716 -16.8875 8 17 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 -21.636kcal/mol
Ligand efficiency (LE) -0.9834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.538
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 292.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.93
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.45kcal/mol
Minimised FF energy 42.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 548.7Ų
Total solvent-accessible surface area of free ligand
BSA total 433.8Ų
Buried surface area upon binding
BSA apolar 350.8Ų
Hydrophobic contacts buried
BSA polar 83.0Ų
Polar contacts buried
Fraction buried 79.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2424.7Ų
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 1386.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)