4QF9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding Mode of an alpha-Amino Acid-Linked Quinoxaline-2,3-dione Analogue at Glutamate Receptor Subtype GluK1.

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

(2015) ACS Chem Neurosci 6: 845-854

  • DOI: 10.1021/acschemneuro.5b00038

  • PubMed 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, ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, kainate 1
A, B, C
257Rattus norvegicusMutation(s): 0 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
35K
Query on 35K

Download SDF File 
Download CCD File 
A, B, C
(2S)-2-amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-yl)butanoic acid
C12 H13 N3 O4
HOBORVHHDCBXLX-ZETCQYMHSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.265α = 90.00
b = 86.802β = 111.62
c = 78.282γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Data collection, Database references
  • Version 1.2: 2017-07-26
    Type: Data collection, Source and taxonomy
  • Version 1.3: 2017-08-09
    Type: Database references