3O29 | pdb_00003o29

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

• PDB DOI: https://doi.org/10.2210/pdb3O29/pdb

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


• Deposited: 2010-07-22 Released: 2010-09-15 
• Deposition Author(s): Maclean, J.K.F., Basten, S., Campbell, R.A., Cumming, I.A., Gillen, K.J., Gillespie, J., Jamieson, C., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Moir, E.M., Morrow, J.A., Papakosta, M., Rankovic, Z., Smith, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

A novel series of positive modulators of the AMPA receptor: discovery and structure based hit-to-lead studies.

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

(2010) Bioorg Med Chem Lett 20: 5753-5756

• PubMed: 20805031 
• DOI: https://doi.org/10.1016/j.bmcl.2010.07.138
• Primary Citation of Related Structures:  
  3O28, 3O29, 3O2A


• PubMed Abstract: 
  

  Starting from an HTS derived hit 1, application of biostructural data facilitated rapid optimization to lead 22, a novel AMPA receptor modulator. This is the first demonstration of how structure based drug design can be exploited in an optimization program for a glutamate receptor.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Motherwell, Lanarkshire ML1 5SH, UK.

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: 30.38 kDa 
• Atom Count: 2,422 
• Modelled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O29	I [auth A]	N-[2-(dimethylamino)ethyl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide C23 H30 F3 N5 O2 S UXUSFGHVYPKOKQ-UHFFFAOYSA-N
GLU	B [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.127	α = 90
b = 88.518	β = 90
c = 47.336	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Maclean, J.K.F., Basten, S., Campbell, R.A., Cumming, I.A., Gillen, K.J., Gillespie, J., Jamieson, C., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Moir, E.M., Morrow, J.A., Papakosta, M., 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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary