5KZQ | pdb_00005kzq

Metabotropic Glutamate Receptor in complex with antagonist (1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.245 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5KZQ

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of (1S,2R,3S,4S,5R,6R)-2-Amino-3-[(3,4-difluorophenyl)sulfanylmethyl]-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylic Acid Hydrochloride (LY3020371HCl): A Potent, Metabotropic Glutamate 2/3 Receptor Antagonist with Antidepressant-Like Activity.

Chappell, M.D.Li, R.Smith, S.C.Dressman, B.A.Tromiczak, E.G.Tripp, A.E.Blanco, M.J.Vetman, T.Quimby, S.J.Matt, J.Britton, T.C.Fivush, A.M.Schkeryantz, J.M.Mayhugh, D.Erickson, J.A.Bures, M.G.Jaramillo, C.Carpintero, M.Diego, J.E.Barberis, M.Garcia-Cerrada, S.Soriano, J.F.Antonysamy, S.Atwell, S.MacEwan, I.Condon, B.Sougias, C.Wang, J.Zhang, A.Conners, K.Groshong, C.Wasserman, S.R.Koss, J.W.Witkin, J.M.Li, X.Overshiner, C.Wafford, K.A.Seidel, W.Wang, X.S.Heinz, B.A.Swanson, S.Catlow, J.T.Bedwell, D.W.Monn, J.A.Mitch, C.H.Ornstein, P.L.

(2016) J Med Chem 59: 10974-10993

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01119
  • Primary Citation Related Structures: 
    5KZN, 5KZQ

  • PubMed Abstract: 

    As part of our ongoing efforts to identify novel ligands for the metabotropic glutamate 2 and 3 (mGlu 2/3 ) receptors, we have incorporated substitution at the C3 and C4 positions of the (1S,2R,5R,6R)-2-amino-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid scaffold to generate mGlu 2/3 antagonists. Exploration of this structure-activity relationship (SAR) led to the identification of (1S,2R,3S,4S,5R,6R)-2-amino-3-[(3,4-difluorophenyl)sulfanylmethyl]-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid hydrochloride (LY3020371·HCl, 19f), a potent, selective, and maximally efficacious mGlu 2/3 antagonist. Further characterization of compound 19f binding to the human metabotropic 2 glutamate (hmGlu 2 ) site was established by cocrystallization of this molecule with the amino terminal domain (ATD) of the hmGlu 2 receptor protein. The resulting cocrystal structure revealed the specific ligand-protein interactions, which likely explain the high affinity of 19f for this site and support its functional mGlu 2 antagonist pharmacology. Further characterization of 19f in vivo demonstrated an antidepressant-like signature in the mouse forced-swim test (mFST) assay when brain levels of this compound exceeded the cellular mGlu 2 IC 50 value.


  • Organizational Affiliation
    • Discovery Chemistry Synthesis Group, Centro de Investigación Lilly S.A. Avda. de la Industria , 30 Alcobendas, Madrid 28108, Spain.

Macromolecule Content 

  • Total Structure Weight: 63.89 kDa 
  • Atom Count: 3,747 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 570 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 2570Homo 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
GTEx:  ENSG00000164082 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14416
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q14416-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6YS

Query on 6YS



Download:Ideal Coordinates CCD File
B [auth A](1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
C15 H15 F2 N O5 S
PVCLSZDVATUGHR-XJDZXMJWSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6YS BindingDB:  5KZQ Ki: 5.3 (nM) from 1 assay(s)
IC50: min: 4.1, max: 16 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.245 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.297α = 90
b = 166.297β = 90
c = 79.776γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary