6F28

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2'-Amino-2'-carboxyethyl]-6-methyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.4A

PDB DOI: https://doi.org/10.2210/pdb6F28/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.222
R-Value Work: 0.195
R-Value Observed: 0.197

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.8b00099
Primary Citation of 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).

Organizational Affiliation

Department of Biotechnology, Chemistry and Pharmacy, (DoE 2018-2022) NatSynDrugs , University of Siena , Via A. Moro 2 , 53100 Siena , Italy.

Macromolecule Content

Total Structure Weight: 59.22 kDa
Atom Count: 4,117
Modelled Residue Count: 506
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3	A, B	258	Rattus norvegicus	Mutation(s): 0 Gene Names: Grik3, Glur7
UniProt
Find proteins for P42264 (Rattus norvegicus) Explore P42264 Go to UniProtKB: P42264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42264
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CG8 Query on CG8 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	(2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5,7-dihydropyrrolo[3,4-d]pyrimidin-1-yl]propanoic acid C₁₀ H₁₄ N₄ O₄ BJXZWHLUHLDGNK-LURJTMIESA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	E [auth A], F [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.222
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.039	α = 90
b = 56.214	β = 90
c = 87.189	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Venskutonyte, R.

Frydenvang, K.

Kastrup, J.S.

Revision History (Full details and data files)

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

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Help and Resources

6F28

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2'-Amino-2'-carboxyethyl]-6-methyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.4A

( 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.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)