› 6leh

X-ray diffraction
2Å resolution

Crystal structure of Autotaxin in complex with an inhibitor

Released:
DOI: 10.2210/pdb6leh/pdb
PDB entry 6leh coloured by chain, front view.
PDB entry 6leh coloured by chain, side view.
PDB entry 6leh coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Identification of Potent In Vivo Autotaxin Inhibitors that Bind to Both Hydrophobic Pockets and Channels in the Catalytic Domain.
Kawaguchi M, Okabe T, Okudaira S, Hama K, Kano K, Nishimasu H, Nakagawa H, Ishitani R, Kojima H, Nureki O, Aoki J, Nagano T
J Med Chem 63 3188-3204 (2020)
PMID: 32134652

Function and Biology Details

Reactions catalysed: 
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
A phosphatidylcholine + H(2)O = choline + a phosphatidate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Autotaxin Chain: A
Molecule details ›
Chain: A
Length: 835 amino acids
Theoretical weight: 96.21 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9R1E6 (Residues: 36-862; Coverage: 99%)
Gene names: Enpp2, Npps2, Pdnp2
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
8 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 1 x CA
Ligand NA 1 x NA
Ligand K 1 x K
Ligand SO4 1 x SO4
Ligand CL 2 x CL
Ligand EDO 17 x EDO
Ligand EAR 1 x EAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 61.507Å b: 94.145Å c: 75.556Å
α: 90° β: 93.92° γ: 90°
R-values:
R R work R free
0.192 0.189 0.237
Expression system: Homo sapiens

Quick links

Citations

1 review citation

Design and Development of Autotaxin Inhibitors.
Jia et al. (2021)
2 other articles