5ELV

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504-N775) in complex with glutamate and BPAM-521 at 1.92 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.

Krintel, C.Francotte, P.Pickering, D.S.Juknaite, L.Phlsgaard, J.Olsen, L.Frydenvang, K.Goffin, E.Pirotte, B.Kastrup, J.S.

(2016) Biophys.J. 110: 2397-2406

  • DOI: 10.1016/j.bpj.2016.04.032

  • PubMed Abstract: 
  • The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a c ...

    The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a cleft formed by the interface of two neighboring ligand binding domains and act by stabilizing the agonist-bound open-channel conformation. The driving forces behind the binding of these modulators can be significantly altered with only minor substitutions to the parent molecules. In this study, we show that changing the 7-fluorine substituent of modulators BPAM97 (2) and BPAM344 (3) into a hydroxyl group (BPAM557 (4) and BPAM521 (5), respectively), leads to a more favorable binding enthalpy (ΔH, kcal/mol) from -4.9 (2) and -7.5 (3) to -6.2 (4) and -14.5 (5), but also a less favorable binding entropy (-TΔS, kcal/mol) from -2.3 (2) and -1.3 (3) to -0.5 (4) and 4.8 (5). Thus, the dissociation constants (Kd, μM) of 4 (11.2) and 5 (0.16) are similar to those of 2 (5.6) and 3 (0.35). Functionally, 4 and 5 potentiated responses of 10 μM L-glutamate at homomeric rat GluA2(Q)i receptors with EC50 values of 67.3 and 2.45 μM, respectively. The binding mode of 5 was examined with x-ray crystallography, showing that the only change compared to that of earlier compounds was the orientation of Ser-497 pointing toward the hydroxyl group of 5. The favorable enthalpy can be explained by the formation of a hydrogen bond from the side-chain hydroxyl group of Ser-497 to the hydroxyl group of 5, whereas the unfavorable entropy might be due to desolvation effects combined with a conformational restriction of Ser-497 and 5. In summary, this study shows a remarkable example of enthalpy-entropy compensation in drug development accompanied with a likely explanation of the underlying structural mechanism.


    Related Citations: 
    • Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold.
      Noerholm, A.B.,Francotte, P.,Olsen, L.,Krintel, C.,Frydenvang, K.,Goffin, E.,Challal, S.,Danober, L.,Botez-Pop, I.,Lestage, P.,Pirotte, B.,Kastrup, J.S.
      (2013) J. Med. Chem. 56: 8736
    • Probing the allosteric modulator binding site of GluR2 with thiazide derivatives.
      Ptak, C.P.,Ahmed, A.H.,Oswald, R.E.
      (2009) Biochemistry 48: 8594
    • Positive allosteric modulators of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid receptors belonging to 4-cyclopropyl-3,4-dihydro-2h-1,2,4-pyridothiadiazine dioxides and diversely chloro-substituted 4-cyclopropyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides.
      Francotte, P.,Noerholm, A.B.,Deva, T.,Olsen, L.,Frydenvang, K.,Goffin, E.,Fraikin, P.,de Tullio, P.,Challal, S.,Thomas, J.Y.,Iop, F.,Louis, C.,Botez-Pop, I.,Lestage, P.,Danober, L.,Kastrup, J.S.,Pirotte, B.
      (2014) J. Med. Chem. 57: 9539
    • Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2.
      Krintel, C.,Frydenvang, K.,Olsen, L.,Kristensen, M.T.,de Barrios, O.,Naur, P.,Francotte, P.,Pirotte, B.,Gajhede, M.,Kastrup, J.S.
      (2012) Biochem. J. 441: 173


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2,Glutamate receptor 2
A, B
264Rattus norvegicusMutation(s): 2 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5PX
Query on 5PX

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A, B
4-Cyclopropyl-3,4-dihydro-7-hydroxy-2H-1,2,4-benzothiadiazine 1,1-dioxide
BPAM-521
C10 H12 N2 O3 S
OMEAYSCNDLQLNC-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.790α = 90.00
b = 122.480β = 90.00
c = 47.540γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection
  • Version 1.3: 2018-03-07
    Type: Source and taxonomy