6ODL | pdb_00006odl

Crystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.283 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Stereoselective synthesis of novel 2'-(S)-CCG-IV analogues as potent NMDA receptor agonists.

Maolanon, A.Papangelis, A.Kawiecki, D.Mou, T.C.Syrenne, J.T.Yi, F.Hansen, K.B.Clausen, R.P.

(2021) Eur J Med Chem 212: 113099-113099

  • DOI: https://doi.org/10.1016/j.ejmech.2020.113099
  • Primary Citation Related Structures: 
    6ODL

  • PubMed Abstract: 

    We developed a versatile stereoselective route for the synthesis of new 2'-(S)-CCG-IV analogues. The route allows for late stage diversification and thereby provides access to a great variety of conformationally restricted cyclopropyl glutamate analogues. A selection of the 2'-(S)-CCG-IV analogues were evaluated using two-electrode voltage-clamp electrophysiology at recombinant GluN1/GluN2A-D receptors, demonstrating that agonists can be developed with GluN2 subunit-dependent potency and agonist efficacy. We also describe a crystal structure of the GluN2A agonist binding domain in complex with 2'-butyl-(S)-CCG-IV that determines the position of 2'-substituents in (S)-CCG-IV agonists in the glutamate binding site and provides further insight to the structural determinants of their agonist efficacy. The stereoselective synthesis described here enables versatile and straight-forward modifications to diverse analogues of interest for the development of potent subtype-specific NMDA receptor agonists and other applications.


  • Organizational Affiliation
    • Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK, 2100, Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 63.14 kDa 
  • Atom Count: 4,596 
  • Modeled Residue Count: 557 
  • Deposited Residue Count: 558 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
A, B
279Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus)
Explore Q00959 
Go to UniProtKB:  Q00959
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00959
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
M7V BindingDB:  6ODL EC50: 2.88e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.283 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.094α = 90
b = 52.094β = 90
c = 197.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103546
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1R01NS097536

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary