7P0K | pdb_00007p0k

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

PDB DOI: https://doi.org/10.2210/pdb7P0K/pdb

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

Deposited: 2021-06-29 Released: 2022-07-13
Deposition Author(s): Salgado-Polo, F., Shao, T., Xiao, Z., Van, R., Chen, J., Rong, J., Haider, A., Shao, Y., Josephson, L., Perrakis, A., Liang, S.H.
Funding Organization(s): Oncode Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.271 (Depositor), 0.289 (DCC)
R-Value Work:
0.212 (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

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

PubMed: 34662125 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.1c00913
Primary Citation 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 [ ¹⁸F] 9j , designated as [ ¹⁸F]ATX-1905 ([ ¹⁸F] 20 ), was designed and proved to be highly stable against in vivo radiodefluorination compared with [ ¹⁸F] 9c , [ ¹⁸F] 9f , [ ¹⁸F] 9h , and [ ¹⁸F] 9j . These results along with in vitro and in vivo studies toward ATX in a mouse model of LPS-induced liver injury suggest that [ ¹⁸F]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.

Macromolecule Content

Total Structure Weight: 91.6 kDa
Atom Count: 6,691
Modeled Residue Count: 770
Deposited Residue Count: 770
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]	770	Rattus norvegicus	Mutation(s): 1 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
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-glucopyranose	B [auth AbA]	7		N/A	Interactions Focus chain B [auth AbA] Interactions & Density Focus chain B [auth AbA]
Glycosylation Resources
GlyTouCan: G19138OU GlyCosmos: G19138OU GlyGen: G19138OU

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4I0 (Subject of Investigation/LOI) Query on 4I0 Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] MOL2 format, chain L [auth AAA] mmCIF format, chain L [auth AAA]	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		Interactions Focus chain L [auth AAA] Interactions & Density Focus chain L [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 K [auth AAA] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA], J [auth AAA], K [auth AAA], M [auth AAA], N [auth AAA]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Interactions & Density Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], G [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain O [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain E [auth AAA]	D [auth AAA], E [auth AAA], O [auth AAA]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain O [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain O [auth AAA]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]