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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acs.jmedchem.7b01722
  • Primary Citation of Related Structures:  
    6FFH, 6FFI

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5444Homo sapiensTequatrovirus T4Mutation(s): 6 
Gene Names: GRM5GPRC1EMGLUR5
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41594P00720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth A],
I [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
D8B
Query on D8B

Download Ideal Coordinates CCD File 
J [auth A]2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine
C15 H13 N O
STDHINPODVHROK-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
D8B BindingDB:  6FFI Ki: min: 10, max: 11 (nM) from 2 assay(s)
IC50: 8 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description