6HCC

STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 1.6 A RESOLUTION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


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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: 10.1021/acsmedchemlett.8b00369
  • Primary Citation of Related Structures:  
    6HCB, 6HCA, 6HCC, 6HCH, 6HC9

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B264Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FXW (Subject of Investigation/LOI)
Query on FXW

Download Ideal Coordinates CCD File 
C [auth A]6,6'-(ETHANE-1,2-DIYL)BIS(4-CYCLOPROPYL-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE)
C22 H26 N4 O4 S2
TVWVZMLPANTKEA-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
D [auth A], R [auth B]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth A], X [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], S [auth B], T [auth B], U [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], V [auth B], W [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
N [auth A], O [auth A], P [auth A], Q [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A], Y [auth B], Z [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FXW BindingDB:  6HCC EC50: min: 1.3, max: 1.4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.979α = 90
b = 121.967β = 90
c = 47.395γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release