5L0B

Crystal Structure of Autotaxin and Compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel Autotaxin Inhibitors for the Treatment of Osteoarthritis Pain: Lead Optimization via Structure-Based Drug Design.

Jones, S.B.Pfeifer, L.A.Bleisch, T.J.Beauchamp, T.J.Durbin, J.D.Klimkowski, V.J.Hughes, N.E.Rito, C.J.Dao, Y.Gruber, J.M.Bui, H.Chambers, M.G.Chandrasekhar, S.Lin, C.McCann, D.J.Mudra, D.R.Oskins, J.L.Swearingen, C.A.Thirunavukkarasu, K.Norman, B.H.

(2016) Acs Med.Chem.Lett. 7: 857-861

  • DOI: 10.1021/acsmedchemlett.6b00207
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In an effort to develop a novel therapeutic agent aimed at addressing the unmet need of patients with osteoarthritis pain, we set out to develop an inhibitor for autotaxin with excellent potency and physical properties to allow for the clinical inves ...

    In an effort to develop a novel therapeutic agent aimed at addressing the unmet need of patients with osteoarthritis pain, we set out to develop an inhibitor for autotaxin with excellent potency and physical properties to allow for the clinical investigation of autotaxin-induced nociceptive and neuropathic pain. An initial hit identification campaign led to an aminopyrimidine series with an autotaxin IC50 of 500 nM. X-ray crystallography enabled the optimization to a lead compound that demonstrated favorable potency (IC50 = 2 nM), PK properties, and a robust PK/PD relationship.


    Organizational Affiliation

    Lilly Research Laboratories , A Division of Eli Lilly and Company, Indianapolis, Indiana 46285, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A, B
871Rattus norvegicusMutation(s): 2 
Gene Names: Enpp2 (Atx, Npps2)
EC: 3.1.4.39
Find proteins for Q64610 (Rattus norvegicus)
Go to UniProtKB:  Q64610
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
6ZM
Query on 6ZM

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Download CCD File 
A, B
1-{2-[(2,3-dihydro-1H-inden-2-yl)amino]-7,8-dihydropyrido[4,3-d]pyrimidin-6(5H)-yl}ethan-1-one
C18 H20 N4 O
YZUQRESBRMOGBQ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.827α = 90.00
b = 96.733β = 112.86
c = 136.284γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-27 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Durbin, J.D.

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references