8C3P | pdb_00008c3p

Crystal structure of autotaxin gamma in complex with LPA 18:1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of potent chromone-based autotaxin inhibitors inspired by cannabinoids.

Eymery, M.C.Nguyen, K.A.Basu, S.Hausmann, J.Tran-Nguyen, V.K.Seidel, H.P.Gutierrez, L.Boumendjel, A.McCarthy, A.A.

(2023) Eur J Med Chem 263: 115944-115944

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115944
  • Primary Citation Related Structures: 
    8C3O, 8C3P, 8C4W, 8C7R

  • PubMed Abstract: 

    Autotaxin (ATX) is an enzyme primarily known for the production of lysophosphatidic acid. Being involved in the development of major human diseases, such as cancer and neurodegenerative diseases, the enzyme has been featured in multiple studies as a pharmacological target. We previously found that the cannabinoid tetrahydrocannabinol (THC) could bind and act as an excellent inhibitor of ATX. This study aims to use the cannabinoid scaffold as a starting point to find cannabinoid-unrelated ATX inhibitors, following a funnel down approach in which large chemical libraries sharing chemical similarities with THC were screened to identify lead scaffold types for optimization. This approach allowed us to identify compounds bearing chromone and indole scaffolds as promising ATX inhibitors. Further optimization led to MEY-003, which is characterized by the direct linkage of an N-pentyl indole to the 5,7-dihydroxychromone moiety. This molecule has potent inhibitory activity towards ATX-β and ATX-ɣ as evidenced by enzymatic studies and its mode of action was rationalized by structural biology studies using macromolecular X-ray crystallography.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France; Univ. Grenoble Alpes, INSERM U1039, LRB, 38000, Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 209.57 kDa 
  • Atom Count: 13,266 
  • Modeled Residue Count: 1,556 
  • Deposited Residue Count: 1,776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A, B
888Homo sapiensMutation(s): 2 
Gene Names: ENPP2ATXPDNP2
EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13822 (Homo sapiens)
Explore Q13822 
Go to UniProtKB:  Q13822
PHAROS:  Q13822
GTEx:  ENSG00000136960 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13822
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q13822-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NKP
(Subject of Investigation/LOI)

Query on NKP



Download:Ideal Coordinates CCD File
F [auth A],
V [auth B]
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
5JK

Query on 5JK



Download:Ideal Coordinates CCD File
E [auth A],
T [auth B]
7alpha-hydroxycholesterol
C27 H46 O2
OYXZMSRRJOYLLO-RVOWOUOISA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
G [auth A]
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
W [auth B],
X [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
U [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth B],
BA [auth B],
L [auth A],
M [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
Y [auth B],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.94α = 90
b = 57.22β = 92.722
c = 287.926γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing
pointlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary