FAIRMol

Z49907357

Pose ID 8759 Compound 3971 Pose 629

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 Z49907357
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.29
Burial
83%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.252
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.339
ADMET + ECO + DL
ADMETscore (GDS)
0.339
absorption · distr. · metab.
DLscore
0.390
drug-likeness
P(SAFE)
0.11
GDS classification
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 (-0.984 kcal/mol/HA) ✓ Good fit quality (FQ -8.82) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (15.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (10)
Score
-23.626
kcal/mol
LE
-0.984
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
24
heavy atoms
MW
329
Da
LogP
5.25
cLogP
Final rank
1.0839
rank score
Inter norm
-1.147
normalised
Contacts
17
H-bonds 3
Strain ΔE
15.8 kcal/mol
SASA buried
83%
Lipo contact
82% BSA apolar/total
SASA unbound
589 Ų
Apolar buried
399 Ų

Interaction summary

HBA 1 HY 3 PI 3 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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 overlap15Native recall0.79
Jaccard0.71RMSD-
HB strict2Strict recall0.22
HB same residue+role2HB role recall0.29
HB same residue2HB residue recall0.29

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
629 1.083864263177904 -1.14674 -23.6257 3 17 15 0.79 0.29 - 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 -23.626kcal/mol
Ligand efficiency (LE) -0.9844kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.822
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 329.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.25
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 97.58kcal/mol
Minimised FF energy 81.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 589.3Ų
Total solvent-accessible surface area of free ligand
BSA total 487.2Ų
Buried surface area upon binding
BSA apolar 399.0Ų
Hydrophobic contacts buried
BSA polar 88.2Ų
Polar contacts buried
Fraction buried 82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2557.7Ų
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 1404.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)