2P2A | pdb_00002p2a

X-ray structure of the GluR2 ligand binding core (S1S2J) in complex with 2-Bn-tet-AMPA at 2.26A resolution

• PDB DOI: https://doi.org/10.2210/pdb2P2A/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-07 Released: 2007-06-19 
• Deposition Author(s): Frydenvang, K., Kastrup, J.S., Gajhede, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.273 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

A tetrazolyl-substituted subtype-selective AMPA receptor agonist.

Vogensen, S.B., Frydenvang, K., Greenwood, J.R., Postorino, G., Nielsen, B., Pickering, D.S., Ebert, B., Bolcho, U., Egebjerg, J., Gajhede, M., Kastrup, J.S., Johansen, T.N., Clausen, R.P., Krogsgaard-Larsen, P.

(2007) J Med Chem 50: 2408-2414

• PubMed: 17455929 
• DOI: https://doi.org/10.1021/jm061439q
• Primary Citation Related Structures: 
  2P2A


• PubMed Abstract: 
  

  Replacement of the methyl group of the AMPA receptor agonist 2-amino-3-[3-hydroxy-5-(2-methyl-2H-5-tetrazolyl)-4-isoxazolyl]propionic acid (2-Me-Tet-AMPA) with a benzyl group provided the first AMPA receptor agonist, compound 7, capable of discriminating GluR2-4 from GluR1 by its more than 10-fold preference for the former receptor subtypes. An X-ray crystallographic analysis of this new analogue in complex with the GluR2-S1S2J construct shows that accommodation of the benzyl group creates a previously unobserved pocket in the receptor, which may explain the remarkable pharmacological profile of compound 7.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, DK-2100 Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 59.21 kDa 
• Atom Count: 4,473 
• Modeled Residue Count: 513 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B	263	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria2
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MP9	G [auth B]	2-AMINO-3-[3-HYDROXY-5-(2-BENZYL-2H-5-TETRAZOLYL)-4-ISOXAZOLYL]-PROPIONIC ACID C14 H14 N6 O4 ZNMNDDBPIVAUGG-JTQLQIEISA-N
GLU	E [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.273 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.12	α = 90
b = 121.98	β = 90
c = 47.2	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Frydenvang, K., Kastrup, J.S., Gajhede, M.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-16
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary