FAIRMol

Z31204478

Pose ID 8606 Compound 4014 Pose 476

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 Z31204478
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
41.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.55, H-bond role recall 0.57
Burial
79%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular 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 (-1.236 kcal/mol/HA) ✓ Good fit quality (FQ -11.07) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Extreme strain energy (41.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-29.660
kcal/mol
LE
-1.236
kcal/mol/HA
Fit Quality
-11.07
FQ (Leeson)
HAC
24
heavy atoms
MW
342
Da
LogP
2.82
cLogP
Final rank
3.3606
rank score
Inter norm
-1.163
normalised
Contacts
15
H-bonds 11
Strain ΔE
41.7 kcal/mol
SASA buried
79%
Lipo contact
63% BSA apolar/total
SASA unbound
558 Ų
Apolar buried
279 Ų

Interaction summary

HBA 9 HY 2 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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: 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 overlap12Native recall0.63
Jaccard0.55RMSD-
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
476 3.3605964785052445 -1.16292 -29.6601 11 15 12 0.63 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 -29.660kcal/mol
Ligand efficiency (LE) -1.2358kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.075
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 342.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.82
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.87kcal/mol
Minimised FF energy 57.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 558.0Ų
Total solvent-accessible surface area of free ligand
BSA total 443.0Ų
Buried surface area upon binding
BSA apolar 278.7Ų
Hydrophobic contacts buried
BSA polar 164.4Ų
Polar contacts buried
Fraction buried 79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2441.3Ų
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 1389.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)