6HCH | pdb_00006hch

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM01 AT 1.6 A RESOLUTION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.178 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor.

Laulumaa, S.Hansen, K.V.Masternak, M.Drapier, T.Francotte, P.Pirotte, B.Frydenvang, K.Kastrup, J.S.

(2019) ACS Med Chem Lett 10: 243-247

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00369
  • Primary Citation Related Structures: 
    6HC9, 6HCA, 6HCB, 6HCC, 6HCH

  • PubMed Abstract: 

    The ionotropic glutamate receptor GluA2 is considered to be an attractive target for positive allosteric modulation for the development of pharmacological tools or cognitive enhancers. Here, we report a detailed structural characterization of two recently reported dimeric positive allosteric modulators, TDPAM01 and TDPAM02, with nanomolar potency at GluA2. Using X-ray crystallography, TDPAM01 and TDPAM02 were crystallized in the ligand-binding domain of the GluA2 flop isoform as well as in the flip-like mutant N775S and the preformed dimer L504Y-N775S. In all structures, one modulator molecule binds at the dimer interface with two characteristic hydrogen bonds being formed from the modulator to Pro515. Whereas the GluA2 dimers and modulator binding mode are similar when crystallized in the presence of l-glutamate, the shape of the binding site differs when no l-glutamate is present. TDPAM02 has no effect on domain closure in both apo and l-glutamate bound GluA2 dimers compared to structures without modulator.


  • Organizational Affiliation
    • Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 91.55 kDa 
  • Atom Count: 7,300 
  • Modeled Residue Count: 788 
  • Deposited Residue Count: 792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C
264Rattus norvegicusMutation(s): 2 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D45
(Subject of Investigation/LOI)

Query on D45



Download:Ideal Coordinates CCD File
LA [auth C],
N [auth A]
6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)
C18 H22 N4 O4 S2
PZUOXMWBXQXKJK-UHFFFAOYSA-N
GLU

Query on GLU



Download:Ideal Coordinates CCD File
CA [auth C],
D [auth A],
T [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
PA [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
Q [auth A],
SA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
DA [auth C]
E [auth A]
EA [auth C]
F [auth A]
FA [auth C]
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
R [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth B]
MA [auth C]
NA [auth C]
O [auth A]
OA [auth C]
AA [auth B],
MA [auth C],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
S [auth A],
Z [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth B],
QA [auth C],
RA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.178 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.63α = 90
b = 163.58β = 90
c = 47.528γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary