FAIRMol

Z50086561

Pose ID 9421 Compound 1971 Pose 613

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 Z50086561
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 strong SASA done
Strain ΔE
14.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.60
Burial
80%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
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 (-0.995 kcal/mol/HA) ✓ Good fit quality (FQ -8.78) ✓ Good H-bonds (3 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (14.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (8)
Score
-22.892
kcal/mol
LE
-0.995
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
23
heavy atoms
MW
309
Da
LogP
1.71
cLogP
Final rank
0.6152
rank score
Inter norm
-0.977
normalised
Contacts
12
H-bonds 6
Strain ΔE
14.8 kcal/mol
SASA buried
80%
Lipo contact
82% BSA apolar/total
SASA unbound
562 Ų
Apolar buried
365 Ų

Interaction summary

HBD 2 HBA 1 HY 2 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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: permissive.
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 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
601 -0.08393370650992972 -1.42493 -32.9767 7 10 0 0.00 0.00 - no Open
613 0.615161706844462 -0.976968 -22.8924 6 12 8 0.53 0.60 - no Current
608 0.6524729591351708 -1.29427 -29.6766 9 11 0 0.00 0.00 - no Open
625 1.3640965411540737 -0.962163 -22.0784 4 12 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 -22.892kcal/mol
Ligand efficiency (LE) -0.9953kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.784
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 309.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.71
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.20kcal/mol
Minimised FF energy 118.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 561.9Ų
Total solvent-accessible surface area of free ligand
BSA total 446.5Ų
Buried surface area upon binding
BSA apolar 365.3Ų
Hydrophobic contacts buried
BSA polar 81.3Ų
Polar contacts buried
Fraction buried 79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2410.9Ų
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 1377.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)