5DEX

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, phenyl-ACEPC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.

Lind, G.E.Mou, T.C.Tamborini, L.Pomper, M.G.De Micheli, C.Conti, P.Pinto, A.Hansen, K.B.

(2017) Proc. Natl. Acad. Sci. U.S.A. --: --

  • DOI: 10.1073/pnas.1707752114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NMDA-type glutamate receptors are ligand-gated ion channels that contribute to excitatory neurotransmission in the central nervous system (CNS). Most NMDA receptors comprise two glycine-binding GluN1 and two glutamate-binding GluN2 subunits (GluN2A-D ...

    NMDA-type glutamate receptors are ligand-gated ion channels that contribute to excitatory neurotransmission in the central nervous system (CNS). Most NMDA receptors comprise two glycine-binding GluN1 and two glutamate-binding GluN2 subunits (GluN2A-D). We describe highly potent ( S )-5-[( R )-2-amino-2-carboxyethyl]-4,5-dihydro-1 H -pyrazole-3-carboxylic acid (ACEPC) competitive GluN2 antagonists, of which ST3 has a binding affinity of 52 nM at GluN1/2A and 782 nM at GluN1/2B receptors. This 15-fold preference of ST3 for GluN1/2A over GluN1/2B is improved compared with NVP-AAM077, a widely used GluN2A-selective antagonist, which we show has 11-fold preference for GluN1/2A over GluN1/2B. Crystal structures of the GluN1/2A agonist binding domain (ABD) heterodimer with bound ACEPC antagonists reveal a binding mode in which the ligands occupy a cavity that extends toward the subunit interface between GluN1 and GluN2A ABDs. Mutational analyses show that the GluN2A preference of ST3 is primarily mediated by four nonconserved residues that are not directly contacting the ligand, but positioned within 12 Å of the glutamate binding site. Two of these residues influence the cavity occupied by ST3 in a manner that results in favorable binding to GluN2A, but occludes binding to GluN2B. Thus, we reveal opportunities for the design of subunit-selective competitive NMDA receptor antagonists by identifying a cavity for ligand binding in which variations exist between GluN2A and GluN2B subunits. This structural insight suggests that subunit selectivity of glutamate-site antagonists can be mediated by mechanisms in addition to direct contributions of contact residues to binding affinity.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy.,Department of Food, Environmental and Nutritional Science, University of Milan, 20133 Milan, Italy kasper.hansen@mso.umt.edu andrea.pinto@unimi.it.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812.,Division of Biological Sciences, University of Montana, Missoula, MT 59812.,Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812; kasper.hansen@mso.umt.edu andrea.pinto@unimi.it.,Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812.,Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical School, Baltimore, MD 21205.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 1
A
292Rattus norvegicusMutation(s): 0 
Gene Names: Grin1 (Nmdar1)
Find proteins for P35439 (Rattus norvegicus)
Go to UniProtKB:  P35439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A
B
283Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus)
Go to UniProtKB:  Q00959
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
5E0
Query on 5E0

Download SDF File 
Download CCD File 
B
5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic acid
C13 H13 N3 O4
MAXWODHGWOEWBN-SNVBAGLBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5E0Ki: 22.6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.629α = 90.00
b = 87.302β = 90.00
c = 122.572γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP20GM103546

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references, Derived calculations
  • Version 1.2: 2017-08-23
    Type: Author supporting evidence, Database references