FAIRMol

Z31213085

Pose ID 9204 Compound 3573 Pose 396

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 Z31213085
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
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
35.0 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.00
Burial
65%
Hydrophobic fit
85%
Reason: 11 internal clashes
11 intramolecular clashes 82% of hydrophobic surface is solvent-exposed (18/22 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
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.835 kcal/mol/HA) ✓ Good fit quality (FQ -7.89) ✓ Deep burial (65% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Very high strain energy (35.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-23.389
kcal/mol
LE
-0.835
kcal/mol/HA
Fit Quality
-7.89
FQ (Leeson)
HAC
28
heavy atoms
MW
390
Da
LogP
3.81
cLogP
Final rank
1.8457
rank score
Inter norm
-0.779
normalised
Contacts
12
H-bonds 4
Strain ΔE
35.0 kcal/mol
SASA buried
65%
Lipo contact
85% BSA apolar/total
SASA unbound
665 Ų
Apolar buried
371 Ų

Interaction summary

HBD 1 HBA 1 HY 1 PI 0 CLASH 0

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
No clash · clashes detected for this pose.

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
500 1.830653708137793 -0.854573 -23.2758 2 15 0 0.00 0.00 - no Open
396 1.8456903992094738 -0.779019 -23.3888 4 12 8 0.53 0.00 - no Current
359 5.118283660172024 -0.898635 -21.5044 8 17 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 -23.389kcal/mol
Ligand efficiency (LE) -0.8353kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.886
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 389.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.81
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 119.57kcal/mol
Minimised FF energy 84.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 664.8Ų
Total solvent-accessible surface area of free ligand
BSA total 434.9Ų
Buried surface area upon binding
BSA apolar 371.4Ų
Hydrophobic contacts buried
BSA polar 63.5Ų
Polar contacts buried
Fraction buried 65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2515.4Ų
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 1413.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)