› 5inh

X-ray diffraction
1.84Å resolution

Crystal structure of Autotaxin/ENPP2 with a covalent fragment

Released:
DOI: 10.2210/pdb5inh/pdb
PDB entry 5inh coloured by chain, front view.
PDB entry 5inh coloured by chain, side view.
PDB entry 5inh coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Repurposing Suzuki Coupling Reagents as a Directed Fragment Library Targeting Serine Hydrolases and Related Enzymes.
Lanier M, Cole DC, Istratiy Y, Klein MG, Schwartz PA, Tjhen R, Jennings A, Hixon MS
J Med Chem 60 5209-5215 (2017)
PMID: 28564542

Function and Biology Details

Reaction catalysed: 
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
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):
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 Chain: A
Molecule details ›
Chain: A
Length: 879 amino acids
Theoretical weight: 100.7 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9R1E6 (Residues: 36-862; Coverage: 99%)
Gene names: Enpp2, Npps2, Pdnp2
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
5 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 1 x CA
Ligand NAG 1 x NAG
Ligand ACT 1 x ACT
Ligand 6C1 1 x 6C1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21
Unit cell:
a: 62.358Å b: 80.745Å c: 76.48Å
α: 90° β: 102.86° γ: 90°
R-values:
R R work R free
0.174 0.172 0.207
Expression system: Spodoptera frugiperda

Quick links

Citations

2 review citations

Boron Chemicals in Drug Discovery and Development: Synthesis and Medicinal Perspective.
Das et al. (2022)
1 more

1 mention without citation

Repurposing Suzuki Coupling Reagents as a Directed Fragment Library Targeting Serine Hydrolases and Related Enzymes.
Lanier et al. (2017)