› 5m0s

X-ray diffraction
2.1Å resolution

Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors

Released:
DOI: 10.2210/pdb5m0s/pdb
PDB entry 5m0s coloured by chain, front view.
PDB entry 5m0s coloured by chain, side view.
PDB entry 5m0s coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators.
Keune WJ, Potjewyd F, Heidebrecht T, Salgado-Polo F, Macdonald SJ, Chelvarajan L, Abdel Latif A, Soman S, Morris AJ, Watson AJ, Jamieson C, Perrakis A
J Med Chem 60 2006-2017 (2017)
PMID: 28165241

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-179148 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Autotaxin Chain: A
Molecule details ›
Chain: A
Length: 827 amino acids
Theoretical weight: 95.04 KDa
Source organism: Rattus norvegicus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q64610 (Residues: 36-887; Coverage: 96%)
  • Best match: Q64610-2 (Residues: 36-862)
Gene names: Atx, Enpp2, Npps2
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
7 bound ligands:
Ligand CA 1 x CA
Ligand ZN 2 x ZN
Ligand IOD 13 x IOD
Ligand 7CW 1 x 7CW
Ligand NA 1 x NA
Ligand SCN 11 x SCN
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 62.826Å b: 88.857Å c: 77.293Å
α: 90° β: 103.08° γ: 90°
R-values:
R R work R free
0.24 0.238 0.286
Expression system: Homo sapiens

Quick links

Citations

1 review citation

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

1 mention without citation

The Structural Binding Mode of the Four Autotaxin Inhibitor Types that Differentially Affect Catalytic and Non-Catalytic Functions.
Salgado-Polo et al. (2019)