FAIRMol

Z94530647

Pose ID 8738 Compound 4046 Pose 608

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 Z94530647
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
41.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.29
Burial
79%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.293 kcal/mol/HA) ✓ Good fit quality (FQ -11.59) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (41.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-31.029
kcal/mol
LE
-1.293
kcal/mol/HA
Fit Quality
-11.59
FQ (Leeson)
HAC
24
heavy atoms
MW
323
Da
LogP
2.69
cLogP
Final rank
4.1680
rank score
Inter norm
-1.146
normalised
Contacts
15
H-bonds 10
Strain ΔE
41.3 kcal/mol
SASA buried
79%
Lipo contact
83% BSA apolar/total
SASA unbound
545 Ų
Apolar buried
357 Ų

Interaction summary

HBD 2 HBA 7 HY 2 PI 2 CLASH 1

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
Jaccard0.62RMSD-
HB strict4Strict recall0.44
HB same residue+role2HB role recall0.29
HB same residue3HB residue recall0.43

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
608 4.1679815785979795 -1.14636 -31.0294 10 15 13 0.68 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 -31.029kcal/mol
Ligand efficiency (LE) -1.2929kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.587
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 323.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.69
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.53kcal/mol
Minimised FF energy 59.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 544.6Ų
Total solvent-accessible surface area of free ligand
BSA total 429.2Ų
Buried surface area upon binding
BSA apolar 357.1Ų
Hydrophobic contacts buried
BSA polar 72.2Ų
Polar contacts buried
Fraction buried 78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2519.6Ų
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 1413.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)