7P0K

Crystal structure of Autotaxin (ENPP2) with 18F-labeled positron emission tomography ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 

Starting Model: experimental
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Literature

Imaging Autotaxin In Vivo with 18 F-Labeled Positron Emission Tomography Ligands

Deng, X.Salgado-Polo, F.Shao, T.Xiao, Z.Van, R.Chen, J.Rong, J.Haider, A.Shao, Y.Josephson, L.Perrakis, A.Liang, S.H.

(2021) J Med Chem 64: 15053-15068

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00913
  • Primary Citation of Related Structures:  
    7P0K

  • PubMed Abstract: 

    Autotaxin (ATX) is a secreted phosphodiesterase that has been implicated in a remarkably wide array of pathologies, especially in fibrosis and cancer. While ATX inhibitors have entered the clinical arena, a validated probe for positron emission tomography (PET) is currently lacking. With the aim to develop a suitable ATX-targeted PET radioligand, we have synthesized a focused library of fluorinated imidazo[1,2- a ]pyridine derivatives, determined their inhibition constants, and confirmed their binding mode by crystallographic analysis. Based on their promising in vitro properties, compounds 9c , 9f , 9h , and 9j were radiofluorinated. Also, a deuterated analog of [ 18 F] 9j , designated as [ 18 F]ATX-1905 ([ 18 F] 20 ), was designed and proved to be highly stable against in vivo radiodefluorination compared with [ 18 F] 9c , [ 18 F] 9f , [ 18 F] 9h , and [ 18 F] 9j . These results along with in vitro and in vivo studies toward ATX in a mouse model of LPS-induced liver injury suggest that [ 18 F]ATX-1905 is a suitable PET probe for the non-invasive quantification of ATX.


  • Organizational Affiliation

    Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital & Department of Radiology, Harvard Medical School, Boston, Massachusetts 02114, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2A [auth AAA]770Rattus norvegicusMutation(s): 1 
Gene Names: Enpp2AtxNpps2
EC: 3.1.4.39
UniProt
Find proteins for Q64610 (Rattus norvegicus)
Explore Q64610 
Go to UniProtKB:  Q64610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64610
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q64610-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth AbA]7N/A
Glycosylation Resources
GlyTouCan:  G19138OU
GlyCosmos:  G19138OU
GlyGen:  G19138OU
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4I0 (Subject of Investigation/LOI)
Query on 4I0

Download Ideal Coordinates CCD File 
L [auth AAA]2-[[2-ethyl-6-[4-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]-2-oxidanylidene-ethyl]piperazin-1-yl]imidazo[1,2-a]pyridin-3-yl]-methyl-amino]-4-(4-fluorophenyl)-2,3-dihydro-1,3-thiazole-5-carbonitrile
C30 H34 F2 N8 O S
HIEJMXWIPDOGLP-RCRUUEGKSA-N
NAG
Query on NAG

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C [auth AAA]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD
Query on IOD

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I [auth AAA],
J [auth AAA],
K [auth AAA],
M [auth AAA],
N [auth AAA]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN
Query on ZN

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F [auth AAA],
G [auth AAA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN
Query on SCN

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D [auth AAA],
E [auth AAA],
O [auth AAA]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth AAA]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.57α = 90
b = 87.149β = 90
c = 145.361γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Oncode InstituteNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description