FAIRMol

Z68348244

Pose ID 8621 Compound 2431 Pose 491

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z68348244
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
41.6 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.57
Burial
77%
Hydrophobic fit
79%
Reason: 8 internal clashes
8 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.935 kcal/mol/HA) ✓ Good fit quality (FQ -8.73) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Extreme strain energy (41.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.259
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-8.73
FQ (Leeson)
HAC
27
heavy atoms
MW
432
Da
LogP
1.83
cLogP
Final rank
3.0183
rank score
Inter norm
-1.033
normalised
Contacts
21
H-bonds 9
Strain ΔE
41.6 kcal/mol
SASA buried
77%
Lipo contact
79% BSA apolar/total
SASA unbound
655 Ų
Apolar buried
398 Ų

Interaction summary

HBA 6 HY 4 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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
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: permissive.
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
Jaccard0.60RMSD-
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
477 0.7155541036721699 -0.928176 -16.984 3 18 0 0.00 0.00 - no Open
491 3.018325912781318 -1.03276 -25.2594 9 21 15 0.79 0.57 - no Current
525 3.5599182069924513 -0.81832 -19.5128 8 13 0 0.00 0.00 - no Open
477 4.4916247339812205 -1.17421 -31.2454 10 19 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 -25.259kcal/mol
Ligand efficiency (LE) -0.9355kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.728
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 432.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.83
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 43.48kcal/mol
Minimised FF energy 1.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.3Ų
Total solvent-accessible surface area of free ligand
BSA total 504.4Ų
Buried surface area upon binding
BSA apolar 397.6Ų
Hydrophobic contacts buried
BSA polar 106.7Ų
Polar contacts buried
Fraction buried 77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2543.4Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1404.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)