3WAV

Crystal Structure of Autotaxin in Complex with Compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 3WAV

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 99724.01

Macromolecule Entities
Molecule Chains Length Organism Details
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 A 831 Mus musculus EC#: 3.1.4.39 IUBMB
Mutation: ΔK571, ΔV572, ΔE573, ΔP574
Gene Name(s): Enpp2 Npps2 Pdnp2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DWV
Query on 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
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SCN
Query on SCN

A THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DWV IC50: 180 - 640 nM (99) BindingDB

IC50: 180 nM  BindingMOAD
IC50: 180 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.188
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 61.51 α = 90.00
b = 94.01 β = 94.52
c = 75.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2013-10-16
    Type: Database references