6FFI

Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



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): 6 
Gene Names: GRM5GPRC1EMGLUR5
EC: 3.2.1.17
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
AL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D8BIC50:  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 = 142.822α = 90
b = 43.424β = 98.93
c = 81.976γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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