4MK0

Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog.

Homan, K.T.Wu, E.Wilson, M.W.Singh, P.Larsen, S.D.Tesmer, J.J.

(2014) Mol Pharmacol 85: 237-248

  • DOI: 10.1124/mol.113.089631
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Recently we identified the serotonin reuptake inhibitor paroxetine as an inhibitor of G protein-coupled receptor kinase 2 (GRK2) that improves cardiac performance in live animals. Paroxetine exhibits up to 50-fold selectivity for GRK2 versus other GR ...

    Recently we identified the serotonin reuptake inhibitor paroxetine as an inhibitor of G protein-coupled receptor kinase 2 (GRK2) that improves cardiac performance in live animals. Paroxetine exhibits up to 50-fold selectivity for GRK2 versus other GRKs. A better understanding of the molecular basis of this selectivity is important for the development of even more selective and potent small molecule therapeutics and chemical genetic probes. We first sought to understand the molecular mechanisms underlying paroxetine selectivity among GRKs. We directly measured the K(D) for paroxetine and assessed its mechanism of inhibition for each of the GRK subfamilies and then determined the atomic structure of its complex with GRK1, the most weakly inhibited GRK tested. Our results suggest that the selectivity of paroxetine for GRK2 largely reflects its lower affinity for adenine nucleotides. Thus, stabilization of off-pathway conformational states unique to GRK2 will likely be key for the development of even more selective inhibitors. Next, we designed a benzolactam derivative of paroxetine that has optimized interactions with the hinge of the GRK2 kinase domain. The crystal structure of this compound in complex with GRK2 confirmed the predicted interactions. Although the benzolactam derivative did not significantly alter potency of inhibition among GRKs, it exhibited 20-fold lower inhibition of serotonin reuptake. However, there was an associated increase in the potency for inhibition of other AGC kinases, suggesting that the unconventional hydrogen bond formed by the benzodioxole ring of paroxetine is better accommodated by GRKs.


    Organizational Affiliation

    Life Sciences Institute and the Departments of Pharmacology and Biological Sciences (K.T.H., E.W., P.S., J.J.G.T.), and Vahlteich Medicinal Chemistry Core and the Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan (M.W.W., S.D.L.).



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-adrenergic receptor kinase 1A640Homo sapiensMutation(s): 0 
Gene Names: ADRBK1BARKBARK1GRK2
EC: 2.7.11.15
Find proteins for P25098 (Homo sapiens)
Explore P25098 
Go to UniProtKB:  P25098
NIH Common Fund Data Resources
PHAROS  P25098
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B339Bos taurusMutation(s): 0 
Gene Names: GNB1
Find proteins for P62871 (Bos taurus)
Explore P62871 
Go to UniProtKB:  P62871
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2G59Bos taurusMutation(s): 0 
Gene Names: GNG2
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29X
Query on 29X

Download CCD File 
A
5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-1H-isoindol-1-one
C20 H19 F N2 O2
SVALMNHLKNCREX-YJBOKZPZSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
29XIC50:  3200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.222α = 90
b = 240.973β = 90
c = 212.083γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description