5CGC

Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile).

Christopher, J.A.Aves, S.J.Bennett, K.A.Dore, A.S.Errey, J.C.Jazayeri, A.Marshall, F.H.Okrasa, K.Serrano-Vega, M.J.Tehan, B.G.Wiggin, G.R.Congreve, M.

(2015) J Med Chem 58: 6653-6664

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00892
  • Primary Citation of Related Structures:  
    5CGC, 5CGD

  • PubMed Abstract: 

    Fragment screening of a thermostabilized mGlu5 receptor using a high-concentration radioligand binding assay enabled the identification of moderate affinity, high ligand efficiency (LE) pyrimidine hit 5. Subsequent optimization using structure-based drug discovery methods led to the selection of 25, HTL14242, as an advanced lead compound for further development. Structures of the stabilized mGlu5 receptor complexed with 25 and another molecule in the series, 14, were determined at resolutions of 2.6 and 3.1 Å, respectively.


  • Organizational Affiliation

    Heptares Therapeutics Ltd. , BioPark, Welwyn Garden City, Hertfordshire AL7 3AX, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5444Homo sapiensTequatrovirus T4Mutation(s): 10 
Gene Names: GRM5GPRC1EMGLUR5
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41594 (Homo sapiens)
Explore P41594 
Go to UniProtKB:  P41594
GTEx:  ENSG00000168959 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41594P00720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
51D BindingDB:  5CGC Ki: min: 0.5, max: 0.83 (nM) from 3 assay(s)
IC50: 2.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.021α = 90
b = 43.818β = 99.2
c = 81.617γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description