FAIRMol

Z56960380

Pose ID 9427 Compound 2466 Pose 619

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 Z56960380
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
15.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.20
Burial
69%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 72% of hydrophobic surface is solvent-exposed (13/18 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 (-0.991 kcal/mol/HA) ✓ Good fit quality (FQ -9.13) ✓ Good H-bonds (5 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (15.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.763
kcal/mol
LE
-0.991
kcal/mol/HA
Fit Quality
-9.13
FQ (Leeson)
HAC
26
heavy atoms
MW
426
Da
LogP
4.91
cLogP
Strain ΔE
15.8 kcal/mol
SASA buried
69%
Lipo contact
74% BSA apolar/total
SASA unbound
620 Ų
Apolar buried
320 Ų

Interaction summary

HB 5 HY 4 PI 0 CLASH 4 ⚠ Exposure 72%

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
72% of hydrophobic surface is solvent-exposed (13/18 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 18 Buried (contacted) 5 Exposed 13 LogP 4.91 H-bonds 5
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.981Score-25.763
Inter norm-0.918Intra norm-0.073
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 8 clashes; 2 protein clashes
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 PRO338 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 overlap7Native recall0.47
Jaccard0.37RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
634 0.7610902009089585 -0.911569 -24.2437 6 15 0 0.00 0.00 - no Open
615 0.9140960673762193 -0.968828 -18.4541 0 15 0 0.00 0.00 - no Open
619 2.980557400356469 -0.918108 -25.7627 5 11 7 0.47 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 -25.763kcal/mol
Ligand efficiency (LE) -0.9909kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.129
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 426.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.91
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.45kcal/mol
Minimised FF energy 141.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 620.5Ų
Total solvent-accessible surface area of free ligand
BSA total 429.1Ų
Buried surface area upon binding
BSA apolar 319.8Ų
Hydrophobic contacts buried
BSA polar 109.3Ų
Polar contacts buried
Fraction buried 69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2417.5Ų
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 1438.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)