7Z3K

Autotaxin in complex with orthosteric site-binder CpdA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Autotaxin facilitates selective LPA receptor signaling.

Salgado-Polo, F.Borza, R.Matsoukas, M.T.Marsais, F.Jagerschmidt, C.Waeckel, L.Moolenaar, W.H.Ford, P.Heckmann, B.Perrakis, A.

(2023) Cell Chem Biol 30: 69-84.e14

  • DOI: 10.1016/j.chembiol.2022.12.006
  • Primary Citation of Related Structures:  
    7Z3K, 7Z3L

  • PubMed Abstract: 
  • Autotaxin (ATX; ENPP2) produces the lipid mediator lysophosphatidic acid (LPA) that signals through disparate EDG (LPA 1-3 ) and P2Y (LPA 4-6 ) G protein-coupled receptors. ATX/LPA promotes several (patho)physiological processes, including in pulmonary fibrosis, thus serving as an attractive drug target ...

    Autotaxin (ATX; ENPP2) produces the lipid mediator lysophosphatidic acid (LPA) that signals through disparate EDG (LPA 1-3 ) and P2Y (LPA 4-6 ) G protein-coupled receptors. ATX/LPA promotes several (patho)physiological processes, including in pulmonary fibrosis, thus serving as an attractive drug target. However, it remains unclear if clinical outcome depends on how different types of ATX inhibitors modulate the ATX/LPA signaling axis. Here, we show that the ATX "tunnel" is crucial for conferring key aspects of ATX/LPA signaling and dictates cellular responses independent of ATX catalytic activity, with a preference for activation of P2Y LPA receptors. The efficacy of the ATX/LPA signaling responses are abrogated more efficiently by tunnel-binding inhibitors, such as ziritaxestat (GLPG1690), compared with inhibitors that exclusively target the active site, as shown in primary lung fibroblasts and a murine model of radiation-induced pulmonary fibrosis. Our results uncover a receptor-selective signaling mechanism for ATX, implying clinical benefit for tunnel-targeting ATX inhibitors.


    Organizational Affiliation

    Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands. Electronic address: a.perrakis@nki.nl.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2A [auth AAA]805Rattus norvegicusMutation(s): 3 
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth AbA]2N/A Oligosaccharides Interaction
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IA0 (Subject of Investigation/LOI)
Query on IA0

Download Ideal Coordinates CCD File 
DA [auth AAA][(2~{S},4~{R})-4-[2-[(3,5-dimethylphenyl)amino]-5,7-dihydropyrrolo[3,4-d]pyrimidin-6-yl]-2-methyl-piperidin-1-yl]-(6-fluoranyl-1~{H}-benzotriazol-5-yl)methanone
C27 H29 F N8 O
HMUPZCBYZUCXOP-FXAWDEMLSA-N
 Ligand Interaction
5JK
Query on 5JK

Download Ideal Coordinates CCD File 
F [auth AAA]7alpha-hydroxycholesterol
C27 H46 O2
OYXZMSRRJOYLLO-RVOWOUOISA-N
 Ligand Interaction
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
 Ligand Interaction
IOD
Query on IOD

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FA [auth AAA],
GA [auth AAA],
H [auth AAA],
I [auth AAA],
IA [auth AAA],
FA [auth AAA],
GA [auth AAA],
H [auth AAA],
I [auth AAA],
IA [auth AAA],
J [auth AAA],
JA [auth AAA],
K [auth AAA],
KA [auth AAA],
L [auth AAA],
LA [auth AAA],
M [auth AAA],
MA [auth AAA],
N [auth AAA],
NA [auth AAA],
OA [auth AAA],
PA [auth AAA]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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AA [auth AAA],
BA [auth AAA],
EA [auth AAA],
HA [auth AAA],
V [auth AAA],
AA [auth AAA],
BA [auth AAA],
EA [auth AAA],
HA [auth AAA],
V [auth AAA],
W [auth AAA],
X [auth AAA],
Y [auth AAA],
Z [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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D [auth AAA],
E [auth AAA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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CA [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA],
R [auth AAA],
CA [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA],
R [auth AAA],
S [auth AAA]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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G [auth AAA]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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T [auth AAA],
U [auth AAA]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.662α = 104.159
b = 62.53β = 98.572
c = 63.638γ = 93.153
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
MolProbitymodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references