7Z0N | pdb_00007z0n

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators

• PDB DOI: https://doi.org/10.2210/pdb7Z0N/pdb

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


• Deposited: 2022-02-23 Released: 2022-05-04 
• Deposition Author(s): Salgado-Polo, F., Clark, J.M., Macdonald, S.J.F., Barrett, T.N., Perrakis, A., Jamieson, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.263 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.202 (DCC) 

Starting Model: experimental

Literature

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators.

Clark, J.M., Salgado-Polo, F., Macdonald, S.J.F., Barrett, T.N., Perrakis, A., Jamieson, C.

(2022) J Med Chem 65: 6338-6351

• PubMed: 35440138 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c00368
• Primary Citation Related Structures: 
  7Z0N


• PubMed Abstract: 
  

  Autotaxin (ATX) facilitates the hydrolysis of lysophosphatidylcholine to lysophosphatidic acid (LPA), a bioactive phospholipid, which facilitates a diverse range of cellular effects in multiple tissue types. Abnormal LPA expression can lead to the progression of diseases such as cancer and fibrosis. Previously, we identified a potent ATX steroid-derived hybrid (partially orthosteric and allosteric) inhibitor which did not form interactions with the catalytic site. Herein, we describe the design, synthesis, and biological evaluation of a focused library of novel steroid-derived analogues targeting the bimetallic catalytic site, representing an entirely unique class of ATX inhibitors of type V designation, which demonstrate significant pathway-relevant biochemical and phenotypic biological effects. The current compounds modulated LPA-mediated ATX allostery and achieved indirect blockage of LPA ₁ internalization, in line with the observed reduction in downstream signaling cascades and chemotaxis induction. These novel type V ATX inhibitors represent a promising tool to inactivate the ATX-LPA signaling axis.

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Organizational Affiliation: 
• Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.
Medicines Design, GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.15 kDa 
• Atom Count: 6,877 
• Modeled Residue Count: 792 
• Deposited Residue Count: 805 
• Unique protein chains: 1

Macromolecules

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): 4  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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q64610-1

Oligosaccharides

Help  

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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth AaA]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G91845HM GlyCosmos: G91845HM GlyGen: G91845HM

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I8K (Subject of Investigation/LOI)	V [auth AAA]	[4-[1-[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]piperidin-4-yl]oxyphenyl]-bis(oxidanyl)-$l^{4}-borane C35 H55 B N O6 PHWWHXAZUYBGQF-KSZJEZMCSA-N
MAN	C [auth AAA]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
IOD	G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	R [auth AAA], S [auth AAA], T [auth AAA], X [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth AAA], E [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN	K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], U [auth AAA], W [auth AAA], Y [auth AAA]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	F [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	P [auth AAA], Q [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.263 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.202 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.788	α = 90
b = 89.607	β = 102.908
c = 77.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
Coot	model building
MolProbity	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Salgado-Polo, F., Clark, J.M., Macdonald, S.J.F., Barrett, T.N., Perrakis, A., Jamieson, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary