3O6I | pdb_00003o6i

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator

• PDB DOI: https://doi.org/10.2210/pdb3O6I/pdb

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


• Deposited: 2010-07-29 Released: 2010-09-15 
• Deposition Author(s): Maclean, J.K.F., Campbell, R.A., Cumming, I.A., Gillen, K.J., Gillespie, J., Jamieson, C., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Martin, F., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

A novel series of positive modulators of the AMPA receptor: structure-based lead optimization.

Jamieson, C., Campbell, R.A., Cumming, I.A., Gillen, K.J., Gillespie, J., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Maclean, J.K., Martin, F., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

(2010) Bioorg Med Chem Lett 20: 6072-6075

• PubMed: 20817521 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.063
• Primary Citation Related Structures: 
  3O6G, 3O6H, 3O6I


• PubMed Abstract: 
  

  Starting from lead compound 1, we demonstrate how X-ray structural data can be used to understand SAR and expediently optimize bioavailability in a novel series of AMPA receptor modulators, furnishing 5 with improved bioavailability and robust in vivo activity.

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Organizational Affiliation: 
• Merck Research Laboratories, MSD, Newhouse, Motherwell, Lanarkshire, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.21 kDa 
• Atom Count: 2,438 
• Modeled Residue Count: 263 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A	263	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria2, Glur2
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
O26	C [auth A]	2-[({3-tert-butyl-4-[(methylamino)methyl]-1H-pyrazol-1-yl}acetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide C20 H29 N5 O2 S ORJNBGRVTFLPLF-UHFFFAOYSA-N
GLU	B [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.24	α = 90
b = 87.8	β = 90
c = 47.38	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Maclean, J.K.F., Campbell, R.A., Cumming, I.A., Gillen, K.J., Gillespie, J., Jamieson, C., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Martin, F., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary