6Y5M | pdb_00006y5m

Crystal structure of mouse Autotaxin in complex with compound 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.195 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Y5M

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Development of autotaxin inhibitors: A series of tetrazole cinnamides.

Thomson, C.G.Le Grand, D.Dowling, M.Beattie, D.Elphick, L.Faller, M.Freeman, M.Hardaker, E.Head, V.Hemmig, R.Hill, J.Lister, A.Pascoe, D.Rieffel, S.Shrestha, B.Steward, O.Zink, F.

(2021) Bioorg Med Chem Lett 31: 127663-127663

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127663
  • Primary Citation Related Structures: 
    6Y5M

  • PubMed Abstract: 

    A series of inhibitors of Autotaxin (ATX) have been developed from a high throughput screening hit, 1a, which shows an alternative binding mode to known catalytic site inhibitors. Selectivity over the hERG channel and microsomal clearance were dependent on the lipophilicity of the compounds, and this was optimised by reduction of clogD whilst maintaining high affinity ATX inhibition. Compound 15a shows good oral exposure, and concentration dependent inhibition of formation of LPA in vivo, as shown in pharmacokinetic-pharmacodynamic (PK/PD) experiments.


  • Organizational Affiliation
    • Global Discovery Chemistry, Novartis Institutes For Biomedical Research, Horsham, UK. Electronic address: chris.thomson@pharmaron-uk.com.

Macromolecule Content 

  • Total Structure Weight: 97.92 kDa 
  • Atom Count: 6,771 
  • Modeled Residue Count: 783 
  • Deposited Residue Count: 829 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2829Mus musculusMutation(s): 0 
Gene Names: Enpp2Npps2Pdnp2
EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt
Find proteins for Q9R1E6 (Mus musculus)
Explore Q9R1E6 
Go to UniProtKB:  Q9R1E6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R1E6
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9R1E6-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G47410OF
GlyCosmos: G47410OF
GlyGen: G47410OF

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O9W
(Subject of Investigation/LOI)

Query on O9W



Download:Ideal Coordinates CCD File
I [auth A](~{E})-3-[4-chloranyl-2-[(5-methyl-1,2,3,4-tetrazol-2-yl)methyl]phenyl]-1-[(2~{R})-4-[(4-fluorophenyl)methyl]-2-methyl-piperazin-1-yl]prop-2-en-1-one
C24 H26 Cl F N6 O
VZLIOCMTERNIPD-DKISHCGFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A],
N [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O9W BindingDB:  6Y5M IC50: 9.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.195 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.257α = 87.55
b = 61.199β = 73.05
c = 67.827γ = 80.76
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary