FAIRMol

Z2235487241

Pose ID 9304 Compound 2278 Pose 496

DB fairmolDocking 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 Z2235487241
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 high Native strong SASA done
Strain ΔE
20.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.60
Burial
71%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
1 protein-contact clashes 100% of hydrophobic surface is solvent-exposed (17/17 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.067 kcal/mol/HA) ✓ Good fit quality (FQ -9.27) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (20.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-23.478
kcal/mol
LE
-1.067
kcal/mol/HA
Fit Quality
-9.27
FQ (Leeson)
HAC
22
heavy atoms
MW
318
Da
LogP
3.81
cLogP
Strain ΔE
20.6 kcal/mol
SASA buried
71%
Lipo contact
83% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
316 Ų

Interaction summary

HB 8 HY 1 PI 0 CLASH 1 ⚠ Exposure 100%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (17/17 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) 0 Exposed 17 LogP 3.81 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/4 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.615Score-23.478
Inter norm-1.093Intra norm0.025
Top1000noExcludedno
Contacts10H-bonds8
Artifact reasongeometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 20.6
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 PRO338 THR241 VAL336

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
Jaccard0.39RMSD-
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
498 0.6056672779323204 -1.10997 -19.372 5 14 0 0.00 0.00 - no Open
496 3.6148298597222523 -1.09267 -23.4778 8 10 7 0.47 0.60 - no Current
464 3.7748799528393917 -1.42615 -25.4875 8 14 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 -23.478kcal/mol
Ligand efficiency (LE) -1.0672kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.265
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 317.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.81
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.04kcal/mol
Minimised FF energy 36.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.6Ų
Total solvent-accessible surface area of free ligand
BSA total 379.9Ų
Buried surface area upon binding
BSA apolar 316.1Ų
Hydrophobic contacts buried
BSA polar 63.7Ų
Polar contacts buried
Fraction buried 71.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2413.2Ų
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 1389.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)