Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99724.01 
• Atom Count: 6673 
• Residue Count: 831 
• Unique protein chains: 1

3WAV

Crystal Structure of Autotaxin in Complex with Compound 10

• DOI: 10.2210/pdb3WAV/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Homo sapiens


• Deposited: 2013-05-09 Released: 2013-07-31 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.797 Å
• R-Value Free: 0.223 
• R-Value Work: 0.188 

Literature

Screening and X-ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe

Kawaguchi, M., Okabe, T., Okudaira, S., Nishimasu, H., Ishitani, R., Kojima, H., Nureki, O., Aoki, J., Nagano, T.

(2013) Acs Chem.Biol. 8: 1713-1721

• PubMed: 23688339 
• DOI: 10.1021/cb400150c
• Primary Citation of Related Structures:  
  3WAY, 3WAX, 3WAW


• PubMed Abstract: 
  

Autotaxin (ATX), also known as ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), was originally identified as a tumor cell autocrine motility factor and was found to be identical to plasma lysophospholipase D, which is the predominant contributor to lysophosphatidic acid (LPA) production from lysophospholipids. ATX is therefore considered to regulate the physiological and pathological roles of LPA, including angiogenesis, lymphocyte trafficking, tissue fibrosis, and cancer cell invasion and metastasis. Thus, it is a potential therapeutic target. Here, we first developed a sensitive and specific ATX fluorescence probe, TG-mTMP, and used it to screen ATX inhibitors in a large chemical library. This probe, which is superior to previously available probes FS-3 and CPF4 in terms of sensitivity or specificity, enabled us to identify several novel ATX inhibitor scaffolds. We solved the crystal structures of ATX complexes with the hit compounds at high resolution (1.75-1.95 Å) and used this information to guide optimization of the structure of a selected inhibitor. The optimized compounds, 3BoA and its derivatives, exhibited potent ATX-inhibitory activity both in vitro and in vivo. These inhibitors are expected to be useful tools to understand the roles of ATX in vitro and in vivo and may also be candidate anti-ATX therapeutic agents.

---

Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	831	Mus musculus	Mutation(s): 0  Gene Names: Enpp2 (Npps2, Pdnp2) EC: 3.1.4.39
Find proteins for Q9R1E6 (Mus musculus) Go to UniProtKB:  Q9R1E6

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
SCN	A	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DWV	A	(5Z)-5-(3,4-dichlorobenzylidene)-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4(5H)-one C15 H15 Cl2 N3 O S BSGZTQWZIBOTMJ-LCYFTJDESA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DWV	IC50: 180 - 640 nM (99) BINDINGDB
DWV	IC50: 180 nM BINDINGMOAD
DWV	IC50: 180 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.797 Å
• R-Value Free: 0.223 
• R-Value Work: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 61.505	α = 90.00
b = 94.015	β = 94.52
c = 75.446	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-09 
• Released Date: 2013-07-31 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

Revision History 

• Version 1.0: 2013-07-31
  Type: Initial release
• Version 1.1: 2013-10-16
  Type: Database references