6FFI

Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 

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:  

  • PubMed Abstract: 
  • Two interesting new X-ray structures of negative allosteric modulator (NAM) ligands for the mGlu <sub>5 </sub> 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.,Heptares Therapeutics Ltd. , BioPark , Welwyn Garden City , Hertfordshire AL7 3AX , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
A
444Enterobacteria phage T4Homo sapiens
This entity is chimeric
Mutation(s): 6 
Gene Names: E, GRM5 (GPRC1E, MGLUR5)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P41594 (Homo sapiens)
Go to Gene View: GRM5
Go to UniProtKB:  P41594
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
D8B
Query on D8B

Download SDF File 
Download CCD File 
A
2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine
C15 H13 N O
STDHINPODVHROK-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.822α = 90.00
b = 43.424β = 98.93
c = 81.976γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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