PDBsum entry 4qf9

Membrane protein

PDB id: 4qf9

Contents

Protein chains

250 a.a.

Ligands

35K ×3

SO4 ×4

PG4 ×2

GOL ×3

ACT

Metals

_CL

Waters ×240

PDB id:

4qf9

Name:

Membrane protein

Title:

Structure of gluk1 ligand-binding domain (s1s2) in complex with (s)-2- amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-yl)butanoic acid at 2.28 a resolution

Structure:

Glutamate receptor ionotropic, kainate 1. Chain: a, b, c. Fragment: unp residues 445-559, 682-820. Synonym: gluk1, glutamate receptor 5, glur-5, glur5. Engineered: yes

Source:

Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Strain: rat. Gene: glur5, grik1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.28Å R-factor: 0.200 R-free: 0.247

Authors:

C.M.Kristensen,K.Frydenvang,J.S.Kastrup

Key ref:

C.S.Demmer et al. (2015). Binding mode of an α-amino acid-linked quinoxaline-2,3-dione analogue at glutamate receptor subtype GluK1. Acs Chem Neurosci, 6, 845-854. PubMed id: 25856736 DOI: 10.1021/acschemneuro.5b00038

Date:

20-May-14 Release date: 22-Apr-15

Protein chains

P22756  (GRIK1_RAT) -  Glutamate receptor ionotropic, kainate 1 from Rattus norvegicus

Seq: 949 a.a.

Struc: 250 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/acschemneuro.5b00038

Acs Chem Neurosci 6:845-854 (2015)

PubMed id: 25856736

Binding mode of an α-amino acid-linked quinoxaline-2,3-dione analogue at glutamate receptor subtype GluK1.

C.S.Demmer, C.Møller, P.M.Brown, L.Han, D.S.Pickering, B.Nielsen, D.Bowie, K.Frydenvang, J.S.Kastrup, L.Bunch.

ABSTRACT

Two α-amino acid-functionalized quinoxalines, 1a (CNG-10301) and 1b (CNG-10300), of a quinoxaline moiety coupled to an amino acid moiety were designed, synthesized, and characterized pharmacologically. While 1a displayed low affinity at native AMPA, KA, and NMDA receptors, and at homomeric GluK1,3 receptors, the affinity for GluK2 was in the midmicromolar range (Ki = 136 μM), 1b displayed low to midmicromolar range binding affinity at all the iGluRs (Ki = 9-126 μM). In functional experiments (outside-out patches excised from transfected HEK293T cells), 100 μM 1a partially blocked GluK1 (33% peak response), while GluK2 was unaffected (96% peak response). Furthermore, 1a was shown not to be an agonist at GluK1 and GluK2 at 100 μM. On the other hand, 100 μM 1b fully antagonized GluK1 (8% peak response) but only partially blocked GluK2 (33% peak response). An X-ray structure at 2.3 Å resolution of 1b in the GluK1-LBD (ligand-binding domain) disclosed an unexpected binding mode compared to the predictions made during the design phase; the quinoxaline moiety remains to act as an amino acid bioisostere, but the amino acid moiety is oriented into a new area within the GluK1 receptor. The structure of the GluK1-LBD with 1b showed a large variation in domain openings of the three molecules from 25° to 49°, demonstrating that the GluK1-LBD is capable of undergoing major domain movements.