FAIRMol

Z57108356

Pose ID 9289 Compound 1997 Pose 481

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 Z57108356
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
18.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.40, Jaccard 0.29, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.285 kcal/mol/HA) ✓ Good fit quality (FQ -9.78) ✓ Good H-bonds (5 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (18.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-20.561
kcal/mol
LE
-1.285
kcal/mol/HA
Fit Quality
-9.78
FQ (Leeson)
HAC
16
heavy atoms
MW
218
Da
LogP
1.69
cLogP
Final rank
2.5846
rank score
Inter norm
-1.514
normalised
Contacts
12
H-bonds 5
Strain ΔE
18.0 kcal/mol
SASA buried
87%
Lipo contact
71% BSA apolar/total
SASA unbound
401 Ų
Apolar buried
249 Ų

Interaction summary

HBD 2 HBA 3 HY 4 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

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
Jaccard0.29RMSD-
HB strict1Strict recall0.17
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
442 0.9710332055049138 -1.73274 -26.6975 7 12 0 0.00 0.00 - no Open
481 2.5845699770094757 -1.51447 -20.561 5 12 6 0.40 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 -20.561kcal/mol
Ligand efficiency (LE) -1.2851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.782
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 16HA

Physicochemical properties
Molecular weight 218.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.69
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 58.35kcal/mol
Minimised FF energy 40.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 401.4Ų
Total solvent-accessible surface area of free ligand
BSA total 348.3Ų
Buried surface area upon binding
BSA apolar 248.6Ų
Hydrophobic contacts buried
BSA polar 99.8Ų
Polar contacts buried
Fraction buried 86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2270.8Ų
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 1372.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)