Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.26 kDa 
• Atom Count: 3492 
• Modelled Residue Count: 410 
• Deposited Residue Count: 444 
• Unique protein chains: 1

6FFI

Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A

• DOI: 10.2210/pdb6FFI/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-01-08 Released: 2018-03-07 
• Deposition Author(s): Christopher, J.A., Orgovan, Z., Congreve, M., Dore, A.S., Errey, J.C., Marshall, F.H., Mason, J.S., Okrasa, K., Rucktooa, P., Serrano-Vega, M.J., Ferenczy, G.G., Keseru, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu5) X-ray Structures.

Christopher, J.A., Orgovan, Z., Congreve, M., Dore, A.S., Errey, J.C., Marshall, F.H., Mason, J.S., Okrasa, K., Rucktooa, P., Serrano-Vega, M.J., Ferenczy, G.G., Keseru, G.M.

(2019) J Med Chem 62: 207-222

• PubMed: 29455526 
• DOI: 10.1021/acs.jmedchem.7b01722
• Primary Citation of Related Structures:  
  6FFI, 6FFH


• PubMed Abstract: 
  

Two interesting new X-ray structures of negative allosteric modulator (NAM) ligands for the mGlu ₅ receptor, M-MPEP (3) and fenobam (4), are reported. The new structures show how the binding of the ligands induces different receptor water channel conformations to previously published structures. The structure of fenobam, where a urea replaces the acetylenic linker in M-MPEP and mavoglurant, reveals a binding mode where the ligand is rotated by 180° compared to a previously proposed docking model. The need for multiple ligand structures for accurate GPCR structure-based drug design is demonstrated by the different growing vectors identified for the head groups of M-MPEP and mavoglurant and by the unexpected water-mediated receptor interactions of a new chemotype represented by fenobam. The implications of the new structures for ligand design are discussed, with extensive analysis of the energetics of the water networks of both pseudoapo and bound structures providing a new design strategy for allosteric modulators.

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Organizational Affiliation: 

Medicinal Chemistry Research Group, Research Centre for Natural Sciences , Hungarian Academy of Sciences , 2 Magyar tudósok körútja , Budapest H-1117 , Hungary.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5	A	444	Homo sapiens, Escherichia virus T4	Mutation(s): 6  Gene Names: GRM5, GPRC1E, MGLUR5, E EC: 3.2.1.17
Find proteins for P41594 (Homo sapiens) Explore P41594  Go to UniProtKB:  P41594
NIH Common Fund Data Resources
PHAROS:  P41594 GTEx:  ENSG00000168959
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	A	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
D8B	A	2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine C15 H13 N O STDHINPODVHROK-UHFFFAOYSA-N
MES	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
D8B	IC50:  8   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.822	α = 90
b = 43.424	β = 98.93
c = 81.976	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-08 
• Released Date: 2018-03-07 
Deposition Author(s): Christopher, J.A., Orgovan, Z., Congreve, M., Dore, A.S., Errey, J.C., Marshall, F.H., Mason, J.S., Okrasa, K., Rucktooa, P., Serrano-Vega, M.J., Ferenczy, G.G., Keseru, G.M.

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references
• Version 1.2: 2018-03-28
  Changes: Data collection, Database references
• Version 1.3: 2019-04-24
  Changes: Data collection, Database references, Source and taxonomy