6F29 | pdb_00006f29

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2-Amino-2-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.6A

• PDB DOI: https://doi.org/10.2210/pdb6F29/pdb

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


• Deposited: 2017-11-23 Released: 2018-02-28 
• Deposition Author(s): Venskutonyte, R., Frydenvang, K., Kastrup, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

( S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic Acid (AMPA) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation.

Brogi, S., Brindisi, M., Butini, S., Kshirsagar, G.U., Maramai, S., Chemi, G., Gemma, S., Campiani, G., Novellino, E., Fiorenzani, P., Pinassi, J., Aloisi, A.M., Gynther, M., Venskutonyte, R., Han, L., Frydenvang, K., Kastrup, J.S., Pickering, D.S.

(2018) J Med Chem 61: 2124-2130

• PubMed: 29451794 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00099
• Primary Citation Related Structures: 
  6F28, 6F29


• PubMed Abstract: 
  

  Starting from 1-4 and 7 structural templates, analogues based on bioisosteric replacements (5a-c vs 1, 2 and 6 vs 7) were synthesized for completing the SAR analysis. Interesting binding properties at GluA2, GluK1, and GluK3 receptors were discovered. The requirements for GluK3 interaction were elucidated by determining the X-ray structures of the GluK3-LBD with 2 and 5c and by computational studies. Antinociceptive potential was demonstrated for GluK1 partial agonist 3 and antagonist 7 (2 mg/kg ip).

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Organizational Affiliation: 
• Department of Biotechnology, Chemistry and Pharmacy, (DoE 2018-2022) NatSynDrugs , University of Siena , Via A. Moro 2 , 53100 Siena , Italy.
Department of Pharmacy , University of Napoli Federico II , Via D. Montesano 49 , 80131 Napoli , Italy.
Department of Medicine, Surgery and Neuroscience , University of Siena , Viale M. Bracci 16 , 53100 Siena , Italy.
School of Pharmacy, Faculty of Health Sciences , University of Eastern Finland , 70211 Kuopio , Finland.
Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , DK-2100 Copenhagen , Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.53 kDa 
• Atom Count: 2,088 
• Modeled Residue Count: 254 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3	A	258	Rattus norvegicus	Mutation(s): 0  Gene Names: Grik3, Glur7
UniProt
Find proteins for P42264 (Rattus norvegicus) Explore P42264  Go to UniProtKB:  P42264

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CGW	B [auth A]	(2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid C9 H11 N3 O4 S PETHBUJXGHVGGK-YFKPBYRVSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.04	α = 90
b = 68.04	β = 90
c = 126.86	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Venskutonyte, R., Frydenvang, K., Kastrup, J.S.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Database references
• Version 1.2: 2018-03-21
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary