FAIRMol

Z57018794

Pose ID 8498 Compound 3908 Pose 368

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z57018794
PDB1F3T↗

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 strong SASA done
Strain ΔE
13.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.57
Burial
84%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.431
ADMET + ECO + DL
ADMETscore (GDS)
0.470
absorption · distr. · metab.
DLscore
0.453
drug-likeness
P(SAFE)
0.25
GDS classification
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Risk
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.192 kcal/mol/HA) ✓ Good fit quality (FQ -10.53) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (13.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.427
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-10.53
FQ (Leeson)
HAC
23
heavy atoms
MW
351
Da
LogP
4.59
cLogP
Final rank
4.3288
rank score
Inter norm
-1.279
normalised
Contacts
16
H-bonds 7
Strain ΔE
13.6 kcal/mol
SASA buried
84%
Lipo contact
74% BSA apolar/total
SASA unbound
545 Ų
Apolar buried
341 Ų

Interaction summary

HBA 7 HY 4 PI 3 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

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.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap13Native recall0.68
Jaccard0.59RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
382 1.6924098352168702 -0.95631 -18.4942 6 10 0 0.00 0.00 - no Open
363 3.6247142487319683 -1.20965 -26.224 10 15 0 0.00 0.00 - no Open
368 4.328768664459939 -1.27885 -27.427 7 16 13 0.68 0.57 - 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 -27.427kcal/mol
Ligand efficiency (LE) -1.1925kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.525
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 351.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.59
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.06kcal/mol
Minimised FF energy 41.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 544.6Ų
Total solvent-accessible surface area of free ligand
BSA total 459.5Ų
Buried surface area upon binding
BSA apolar 341.1Ų
Hydrophobic contacts buried
BSA polar 118.5Ų
Polar contacts buried
Fraction buried 84.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2493.1Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1394.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)