5LIA

Crystal structure of murine autotaxin in complex with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of potent inhibitors of the lysophospholipase autotaxin.

Shah, P.Cheasty, A.Foxton, C.Raynham, T.Farooq, M.Gutierrez, I.F.Lejeune, A.Pritchard, M.Turnbull, A.Pang, L.Owen, P.Boyd, S.Stowell, A.Jordan, A.Hamilton, N.M.Hitchin, J.R.Stockley, M.MacDonald, E.Quesada, M.J.Trivier, E.Skeete, J.Ovaa, H.Moolenaar, W.H.Ryder, H.

(2016) Bioorg. Med. Chem. Lett. 26: 5403-5410

  • DOI: 10.1016/j.bmcl.2016.10.036

  • PubMed Abstract: 
  • The autotaxin-lysophosphatidic acid (ATX-LPA) axis has been implicated in several disease conditions including inflammation, fibrosis and cancer. This makes ATX an attractive drug target and its inhibition may lead to useful therapeutic agents. Throu ...

    The autotaxin-lysophosphatidic acid (ATX-LPA) axis has been implicated in several disease conditions including inflammation, fibrosis and cancer. This makes ATX an attractive drug target and its inhibition may lead to useful therapeutic agents. Through a high throughput screen (HTS) we identified a series of small molecule inhibitors of ATX which have subsequently been optimized for potency, selectivity and developability properties. This has delivered drug-like compounds such as 9v (CRT0273750) which modulate LPA levels in plasma and are suitable for in vivo studies. X-ray crystallography has revealed that these compounds have an unexpected binding mode in that they do not interact with the active site zinc ions but instead occupy the hydrophobic LPC pocket extending from the active site of ATX together with occupying the LPA 'exit' channel.


    Organizational Affiliation

    Cancer Research Technology, Discovery Laboratories, Babraham Research Campus, Cambridge CB22 3AT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A
838Mus musculusMutation(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 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
6XN
Query on 6XN

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A
~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]-3-[3-[[4-(trifluoromethyloxy)phenyl]methyl]imidazo[4,5-b]pyridin-2-yl]propanamide
C25 H22 Cl F3 N4 O2
HXYXHSDYBDFOFO-INIZCTEOSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.160α = 85.77
b = 61.580β = 72.68
c = 66.140γ = 80.21
Software Package:
Software NamePurpose
xia2data reduction
PHASERphasing
REFMACrefinement
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references