FAIRMol

Z49539235

Pose ID 8744 Compound 2672 Pose 614

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 Z49539235
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
11.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.57
Burial
75%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 46% of hydrophobic surface appears solvent-exposed (6/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 (-1.366 kcal/mol/HA) ✓ Good fit quality (FQ -11.20) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (11.8 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (12) ✗ Internal clashes (8)
Score
-25.957
kcal/mol
LE
-1.366
kcal/mol/HA
Fit Quality
-11.20
FQ (Leeson)
HAC
19
heavy atoms
MW
321
Da
LogP
3.01
cLogP
Final rank
1.3344
rank score
Inter norm
-1.502
normalised
Contacts
14
H-bonds 11
Strain ΔE
11.8 kcal/mol
SASA buried
75%
Lipo contact
83% BSA apolar/total
SASA unbound
521 Ų
Apolar buried
326 Ų

Interaction summary

HBD 2 HBA 7 HY 2 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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
Jaccard0.65RMSD-
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
598 -0.28913293508711024 -1.6235 -31.4971 6 15 0 0.00 0.00 - no Open
614 1.3344248732509663 -1.50242 -25.9569 11 14 13 0.68 0.57 - no Current
611 2.2747942613675125 -1.27288 -25.5924 6 15 0 0.00 0.00 - no Open
623 3.5490543784675803 -1.26315 -19.672 10 12 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 -25.957kcal/mol
Ligand efficiency (LE) -1.3662kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.198
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 321.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.01
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 64.05kcal/mol
Minimised FF energy 52.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 520.6Ų
Total solvent-accessible surface area of free ligand
BSA total 390.6Ų
Buried surface area upon binding
BSA apolar 325.6Ų
Hydrophobic contacts buried
BSA polar 65.0Ų
Polar contacts buried
Fraction buried 75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2494.3Ų
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 1422.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)