7Z3K | pdb_00007z3k

Autotaxin in complex with orthosteric site-binder CpdA

PDB DOI: https://doi.org/10.2210/pdb7Z3K/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-03-02 Released: 2023-01-25
Deposition Author(s): Salgado-Polo, F., Ford, P., Heckmann, B., Perrakis, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor), 0.228 (DCC)
R-Value Work:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 36640760 Search on PubMed
DOI: https://doi.org/10.1016/j.chembiol.2022.12.006
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 97.65 kDa
Atom Count: 7,130
Modeled Residue Count: 792
Deposited Residue Count: 805
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A [auth AAA]	805	Rattus norvegicus	Mutation(s): 3 Gene Names: Enpp2, Atx, Npps2 EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610 Go to UniProtKB: Q64610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64610
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth AAA]	Go to GlyGen: Q64610-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth AbA]	2		N/A	Interactions Focus chain B [auth AbA] Interactions & Density Focus chain B [auth AbA]
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IA0 (Subject of Investigation/LOI) Query on IA0 Download:Ideal Coordinates CCD File SDF format, chain DA [auth AAA] MOL2 format, chain DA [auth AAA] mmCIF format, chain DA [auth AAA]	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		Interactions Focus chain DA [auth AAA] Interactions & Density Focus chain DA [auth AAA]
5JK Query on 5JK Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	7alpha-hydroxycholesterol C₂₇ H₄₆ O₂ OYXZMSRRJOYLLO-RVOWOUOISA-N		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain PA [auth AAA] SDF format, chain OA [auth AAA] SDF format, chain NA [auth AAA] SDF format, chain N [auth AAA] SDF format, chain MA [auth AAA] SDF format, chain M [auth AAA] SDF format, chain LA [auth AAA] SDF format, chain L [auth AAA] SDF format, chain KA [auth AAA] SDF format, chain K [auth AAA] SDF format, chain JA [auth AAA] SDF format, chain J [auth AAA] SDF format, chain IA [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain GA [auth AAA] SDF format, chain FA [auth AAA] MOL2 format, chain PA [auth AAA] MOL2 format, chain OA [auth AAA] MOL2 format, chain NA [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain MA [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain LA [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain KA [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain JA [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain IA [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain GA [auth AAA] MOL2 format, chain FA [auth AAA] mmCIF format, chain PA [auth AAA] mmCIF format, chain OA [auth AAA] mmCIF format, chain NA [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain MA [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain LA [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain KA [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain JA [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain IA [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain GA [auth AAA] mmCIF format, chain FA [auth AAA]	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		Interactions Focus chain FA [auth AAA] Focus chain GA [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain IA [auth AAA] Focus chain J [auth AAA] Focus chain JA [auth AAA] Focus chain K [auth AAA] Focus chain KA [auth AAA] Focus chain L [auth AAA] Focus chain LA [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth AAA] Focus chain N [auth AAA] Focus chain NA [auth AAA] Focus chain OA [auth AAA] Focus chain PA [auth AAA] Interactions & Density Focus chain FA [auth AAA] Focus chain GA [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain IA [auth AAA] Focus chain J [auth AAA] Focus chain JA [auth AAA] Focus chain K [auth AAA] Focus chain KA [auth AAA] Focus chain L [auth AAA] Focus chain LA [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth AAA] Focus chain N [auth AAA] Focus chain NA [auth AAA] Focus chain OA [auth AAA] Focus chain PA [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth AAA] SDF format, chain Y [auth AAA] SDF format, chain X [auth AAA] SDF format, chain W [auth AAA] SDF format, chain V [auth AAA] SDF format, chain HA [auth AAA] SDF format, chain EA [auth AAA] SDF format, chain BA [auth AAA] SDF format, chain AA [auth AAA] MOL2 format, chain Z [auth AAA] MOL2 format, chain Y [auth AAA] MOL2 format, chain X [auth AAA] MOL2 format, chain W [auth AAA] MOL2 format, chain V [auth AAA] MOL2 format, chain HA [auth AAA] MOL2 format, chain EA [auth AAA] MOL2 format, chain BA [auth AAA] MOL2 format, chain AA [auth AAA] mmCIF format, chain Z [auth AAA] mmCIF format, chain Y [auth AAA] mmCIF format, chain X [auth AAA] mmCIF format, chain W [auth AAA] mmCIF format, chain V [auth AAA] mmCIF format, chain HA [auth AAA] mmCIF format, chain EA [auth AAA] mmCIF format, chain BA [auth AAA] mmCIF format, chain AA [auth AAA]	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		Interactions Focus chain AA [auth AAA] Focus chain BA [auth AAA] Focus chain EA [auth AAA] Focus chain HA [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA] Interactions & Density Focus chain AA [auth AAA] Focus chain BA [auth AAA] Focus chain EA [auth AAA] Focus chain HA [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA], E [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain S [auth AAA] SDF format, chain R [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain P [auth AAA] SDF format, chain O [auth AAA] SDF format, chain CA [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain CA [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain CA [auth AAA]	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		Interactions Focus chain CA [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Interactions & Density Focus chain CA [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain U [auth AAA] SDF format, chain T [auth AAA] MOL2 format, chain U [auth AAA] MOL2 format, chain T [auth AAA] mmCIF format, chain U [auth AAA] mmCIF format, chain T [auth AAA]	T [auth AAA], U [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth AAA] Focus chain U [auth AAA] Interactions & Density Focus chain T [auth AAA] Focus chain U [auth AAA]