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

• PDB DOI: https://doi.org/10.2210/pdb5CGC/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2015-07-09 Released: 2015-08-12 
• Deposition Author(s): 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.

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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

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

• PubMed: 26225459 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.43 kDa 
• Atom Count: 3,359 
• Modelled Residue Count: 409 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5	A	444	Homo sapiens, Tequatrovirus T4	Mutation(s): 10  Gene Names: GRM5, GPRC1E, MGLUR5 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
PHAROS:  P41594 GTEx:  ENSG00000168959
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P41594P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
51D	G [auth A]	3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile C14 H7 Cl F N5 UPDNOLJVPHHECL-UHFFFAOYSA-N
OLA	B [auth A], C [auth A], D [auth A], E [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 143.021	α = 90
b = 43.818	β = 99.2
c = 81.617	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): 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.

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
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary