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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1021/acs.jmedchem.5b00892
  • Primary Citation of Related Structures:  
    5CGD, 5CGC

  • 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 ...

    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.


    Related Citations: 
    • Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain.
      Dore, A.S., Okrasa, K., Patel, J.C., Serrano-Vega, M., Bennett, K., Cooke, R.M., Errey, J.C., Jazayeri, A., Khan, S., Tehan, B., Weir, M., Wiggin, G.R., Marshall, F.H.
      (2014) Nature 511: 557

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5A444Homo sapiensEscherichia virus T4Mutation(s): 10 
Gene Names: GRM5GPRC1EMGLUR5
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class C
Protein: 
Class C GPCR Metabotropic Glutamate Receptor 5 (mGlu5) with bound compound 14
Find proteins for P41594 (Homo sapiens)
Explore P41594 
Go to UniProtKB:  P41594
NIH Common Fund Data Resources
PHAROS  P41594
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
51D
Query on 51D

Download CCD File 
A
3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile
C14 H7 Cl F N5
UPDNOLJVPHHECL-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
51DIC50:  2.5   nM  BindingDB
51DKi:  0.5   nM  BindingDB
51DKi:  0.8299999833106995   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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