4XAQ

mGluR2 ECD and mGluR3 ECD with ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and Pharmacological Characterization of C4-Disubstituted Analogs of 1S,2S,5R,6S-2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylate: Identification of a Potent, Selective Metabotropic Glutamate Receptor Agonist and Determination of Agonist-Bound Human mGlu2 and mGlu3 Amino Terminal Domain Structures.

Monn, J.A.Prieto, L.Taboada, L.Pedregal, C.Hao, J.Reinhard, M.R.Henry, S.S.Goldsmith, P.J.Beadle, C.D.Walton, L.Man, T.Rudyk, H.Clark, B.Tupper, D.Baker, S.R.Lamas, C.Montero, C.Marcos, A.Blanco, J.Bures, M.Clawson, D.K.Atwell, S.Lu, F.Wang, J.Russell, M.Heinz, B.A.Wang, X.Carter, J.H.Xiang, C.Catlow, J.T.Swanson, S.Sanger, H.Broad, L.M.Johnson, M.P.Knopp, K.L.Simmons, R.M.Johnson, B.G.Shaw, D.B.McKinzie, D.L.

(2015) J Med Chem 58: 1776-1794

  • DOI: 10.1021/jm501612y
  • Primary Citation of Related Structures:  
    4XAQ, 4XAR, 4XAS

  • PubMed Abstract: 
  • As part of our ongoing research to identify novel agents acting at metabotropic glutamate 2 (mGlu2) and 3 (mGlu3) receptors, we have previously reported the identification of the C4α-methyl analog of mGlu2/3 receptor agonist 1 (LY354740). This molecule, 1S,2S,4R,5R,6S-2-amino-4-methylbicyclo[3 ...

    As part of our ongoing research to identify novel agents acting at metabotropic glutamate 2 (mGlu2) and 3 (mGlu3) receptors, we have previously reported the identification of the C4α-methyl analog of mGlu2/3 receptor agonist 1 (LY354740). This molecule, 1S,2S,4R,5R,6S-2-amino-4-methylbicyclo[3.1.0]hexane-2,6-dicarboxylate 2 (LY541850), exhibited an unexpected mGlu2 agonist/mGlu3 antagonist pharmacological profile, whereas the C4β-methyl diastereomer (3) possessed dual mGlu2/3 receptor agonist activity. We have now further explored this structure-activity relationship through the preparation of cyclic and acyclic C4-disubstituted analogs of 1, leading to the identification of C4-spirocyclopropane 5 (LY2934747), a novel, potent, and systemically bioavailable mGlu2/3 receptor agonist which exhibits both antipsychotic and analgesic properties in vivo. In addition, through the combined use of protein-ligand X-ray crystallography employing recombinant human mGlu2/3 receptor amino terminal domains, molecular modeling, and site-directed mutagenesis, a molecular basis for the observed pharmacological profile of compound 2 is proposed.


    Organizational Affiliation

    Discovery Chemistry Research and Technologies, ‡Quantitative Biology, §Structural Biology, ∥Drug Disposition, and ⊥Neuroscience Research, Eli Lilly and Company , Indianapolis, Indiana 46285, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 2A, B503Homo sapiensMutation(s): 0 
Gene Names: GRM2GPRC1BMGLUR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14416 (Homo sapiens)
Explore Q14416 
Go to UniProtKB:  Q14416
PHAROS:  Q14416
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14416
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
40F
Query on 40F

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid
C8 H11 N O4
VTAARTQTOOYTES-RGDLXGNYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
40F BindingDB:  4XAQ Ki: min: 11, max: 476 (nM) from 9 assay(s)
IC50: min: 5.6, max: 7 (nM) from 2 assay(s)
EC50: min: 5.1, max: 35 (nM) from 9 assay(s)
Binding MOAD:  4XAQ Ki: 71.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.644α = 90
b = 159.652β = 90
c = 93.88γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2014-12-15 
  • Released Date: 2015-02-04 
  • Deposition Author(s): Clawson, D.K.

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy