3RN8

Crystal Structure of iGluR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and functional analysis of two new positive allosteric modulators of GluA2 desensitization and deactivation.

Timm, D.E.Benveniste, M.Weeks, A.M.Nisenbaum, E.S.Partin, K.M.

(2011) Mol Pharmacol 80: 267-280

  • DOI: https://doi.org/10.1124/mol.110.070243
  • Primary Citation of Related Structures:  
    3RN8, 3RNN

  • PubMed Abstract: 

    At the dimer interface of the extracellular ligand-binding domain of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors a hydrophilic pocket is formed that is known to interact with two classes of positive allosteric modulators, represented by cyclothiazide and the ampakine 2H,3H,6aH-pyrrolidino(2,1-3',2')1,3-oxazino(6',5'-5,4)benzo(e)1,4-dioxan-10-one (CX614). Here, we present structural and functional data on two new positive allosteric modulators of AMPA receptors, phenyl-1,4-bis-alkylsulfonamide (CMPDA) and phenyl-1,4-bis-carboxythiophene (CMPDB). Crystallographic data show that these compounds bind within the modulator-binding pocket and that substituents of each compound overlap with distinct moieties of cyclothiazide and CX614. The goals of the present study were to determine 1) the degree of modulation by CMPDA and CMPDB of AMPA receptor deactivation and desensitization; 2) whether these compounds are splice isoform-selective; and 3) whether predictions of mechanism of action could be inferred by comparing molecular interactions between the ligand-binding domain and each compound with those of cyclothiazide and CX614. CMPDB was found to be more isoform-selective than would be predicted from initial binding assays. It is noteworthy that these new compounds are both more potent and more effective and may be more clinically relevant than the AMPA receptor modulators described previously.


  • Organizational Affiliation

    Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C
280Homo sapiensMutation(s): 0 
Gene Names: GRIA2GLUR2
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens)
Explore P42262 
Go to UniProtKB:  P42262
PHAROS:  P42262
GTEx:  ENSG00000120251 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42262
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RN8
Query on RN8

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid)
C22 H16 N2 O4 S2
BWTPBGGGXPNPMW-UHFFFAOYSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
M [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
J [auth B],
N [auth C],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
K [auth B],
P [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.889α = 90
b = 163.232β = 90
c = 47.356γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2011-05-25 
  • Deposition Author(s): Timm, D.E.

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary