8C3O | pdb_00008c3o

Crystal structure of autotaxin gamma and compound MEY-003

PDB DOI: https://doi.org/10.2210/pdb8C3O/pdb

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

Deposited: 2022-12-27 Released: 2023-11-22
Deposition Author(s): Eymery, M.C., McCarthy, A.A.
Funding Organization(s): European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.271 (Depositor), 0.268 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 37976710 Search on PubMed
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: 212.09 kDa
Atom Count: 13,027
Modeled Residue Count: 1,562
Deposited Residue Count: 1,776
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A, B	888	Homo sapiens	Mutation(s): 2 Gene Names: ENPP2, ATX, PDNP2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13822
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q13822-1
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5JK Query on 5JK Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain E [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain E [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain E [auth A]	E [auth A], IA [auth B]	7alpha-hydroxycholesterol C₂₇ H₄₆ O₂ OYXZMSRRJOYLLO-RVOWOUOISA-N		Interactions Focus chain E [auth A] Focus chain IA [auth B] Interactions & Density Focus chain E [auth A] Focus chain IA [auth B]
T8R (Subject of Investigation/LOI) Query on T8R Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain F [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain F [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain F [auth A]	F [auth A], JA [auth B]	5,7-bis(oxidanyl)-2-(1-pentylindol-3-yl)chromen-4-one C₂₂ H₂₁ N O₄ RZGZFONKKPMOLH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain JA [auth B] Interactions & Density Focus chain F [auth A] Focus chain JA [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain YA [auth B] SDF format, chain Y [auth A] SDF format, chain XA [auth B] SDF format, chain X [auth A] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CB [auth B] SDF format, chain CA [auth A] SDF format, chain BB [auth B] SDF format, chain BA [auth A] SDF format, chain AB [auth B] SDF format, chain AA [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], EA [auth A], FA [auth A], GA [auth A], M [auth A], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], KA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], LA [auth B], MA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain DB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain DB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain DB [auth B]	DB [auth B], HA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DB [auth B] Focus chain HA [auth A] Interactions & Density Focus chain DB [auth B] Focus chain HA [auth A]