FAIRMol

Z57676781

Pose ID 9448 Compound 1853 Pose 640

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 Z57676781
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 high Native mixed SASA done
Strain ΔE
8.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.00
Burial
76%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
2 protein-contact clashes 94% of hydrophobic surface is solvent-exposed (15/16 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 (-0.815 kcal/mol/HA) ✓ Good fit quality (FQ -7.30) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (8.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-19.547
kcal/mol
LE
-0.815
kcal/mol/HA
Fit Quality
-7.30
FQ (Leeson)
HAC
24
heavy atoms
MW
379
Da
LogP
4.77
cLogP
Strain ΔE
8.3 kcal/mol
SASA buried
76%
Lipo contact
75% BSA apolar/total
SASA unbound
593 Ų
Apolar buried
339 Ų

Interaction summary

HB 2 HY 3 PI 0 CLASH 2 ⚠ Exposure 93%

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
94% of hydrophobic surface is solvent-exposed (15/16 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 16 Buried (contacted) 1 Exposed 15 LogP 4.77 H-bonds 2
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (3/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.823Score-19.547
Inter norm-0.945Intra norm0.131
Top1000noExcludedno
Contacts12H-bonds2
Artifact reasongeometry warning; 7 clashes; 2 protein clashes
Residues
ARG242 ARG337 ASP243 ASP385 ASP47 GLU384 LEU339 PHE383 SER282 THR241 VAL335 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 overlap8Native recall0.53
Jaccard0.42RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
646 1.7793144131990835 -1.06676 -25.5714 3 10 0 0.00 0.00 - no Open
640 2.8232917357122225 -0.945054 -19.5474 2 12 8 0.53 0.00 - no Current
653 4.513969588477552 -0.960122 -20.5267 7 19 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 -19.547kcal/mol
Ligand efficiency (LE) -0.8145kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.299
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 379.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.77
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 8.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.07kcal/mol
Minimised FF energy 76.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 592.8Ų
Total solvent-accessible surface area of free ligand
BSA total 451.4Ų
Buried surface area upon binding
BSA apolar 339.4Ų
Hydrophobic contacts buried
BSA polar 112.0Ų
Polar contacts buried
Fraction buried 76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2406.4Ų
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 1423.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)