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 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1016/j.bmcl.2016.10.036
  • Primary Citation of Related Structures:  
    5LIA

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2838Mus musculusMutation(s): 0 
Gene Names: Enpp2Npps2Pdnp2
EC: 3.1.4.39
UniProt
Find proteins for Q9R1E6 (Mus musculus)
Explore Q9R1E6 
Go to UniProtKB:  Q9R1E6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R1E6
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47410OF
GlyCosmos:  G47410OF
GlyGen:  G47410OF
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6XN
Query on 6XN

Download Ideal Coordinates CCD File 
D [auth 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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
J [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6XN BindingDB:  5LIA IC50: min: 1, max: 38 (nM) from 3 assay(s)
EC50: 25 (nM) from 1 assay(s)
Binding MOAD:  5LIA IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.16α = 85.77
b = 61.58β = 72.68
c = 66.14γ = 80.21
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary