Ligand profile

UD6

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_03793 — Uridine diphosphate galacturonate 4-epimerase in cps region

Via homolog PDB 3ruh UniProt Q7BJX9 Formula C₁₈H₂₈N₂O₁₇P₂
Mol. weight 606.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UD6
PDB
3ruh
UniProt (similar protein)
Q7BJX9
Target protein
KP13_03793

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 606.37 Da
LogP (Crippen) -3.56
H-bond donors 8
H-bond acceptors 16
TPSA 293.83 Ų
Rotatable bonds 11
Aromatic rings 1 / 3
Heavy atoms 39
Fraction sp³ C 0.72
Formula C₁₈H₂₈N₂O₁₇P₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 293.8
  • −1 ≤ LogP ≤ 5 -3.56
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 606.4
  • LogP ≤ 5 -3.56
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 293.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)C[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
InChI 
InChI=1S/C18H28N2O17P2/c1-7(22)4-8-12(24)13(25)9(5-21)35-17(8)36-39(31,32)37-38(29,30)33-6-10-14(26)15(27)16(34-10)20-3-2-11(23)19-18(20)28/h2-3,8-10,12-17,21,24-27H,4-6H2,1H3,(H,29,30)(H,31,32)(H,19,23,28)/t8-,9-,10-,12-,13+,14-,15-,16-,17-/m1/s1
InChIKey 
ODPRJDNNGDXFOQ-YIUJVFLPSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01370

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03793.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)