FAIRMol

Z44851669

Pose ID 8785 Compound 3994 Pose 655

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 Z44851669
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 high Native strong SASA done
Strain ΔE
20.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.52, H-bond role recall 0.43
Burial
76%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (8/16 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 Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.126 kcal/mol/HA) ✓ Good fit quality (FQ -9.61) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (20.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-23.651
kcal/mol
LE
-1.126
kcal/mol/HA
Fit Quality
-9.61
FQ (Leeson)
HAC
21
heavy atoms
MW
278
Da
LogP
3.08
cLogP
Final rank
2.7770
rank score
Inter norm
-1.309
normalised
Contacts
13
H-bonds 9
Strain ΔE
20.5 kcal/mol
SASA buried
76%
Lipo contact
81% BSA apolar/total
SASA unbound
523 Ų
Apolar buried
323 Ų

Interaction summary

HBA 9 HY 2 PI 2 CLASH 2

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 overlap11Native recall0.58
Jaccard0.52RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
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
652 2.31847536929549 -0.940081 -19.7377 7 7 0 0.00 0.00 - no Open
655 2.7769847736920648 -1.30879 -23.6512 9 13 11 0.58 0.43 - 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 -23.651kcal/mol
Ligand efficiency (LE) -1.1262kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.606
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 278.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.08
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 111.01kcal/mol
Minimised FF energy 90.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 522.5Ų
Total solvent-accessible surface area of free ligand
BSA total 397.1Ų
Buried surface area upon binding
BSA apolar 323.1Ų
Hydrophobic contacts buried
BSA polar 74.0Ų
Polar contacts buried
Fraction buried 76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2504.7Ų
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 1403.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)