5WG4

Human GRK2 in complex with Gbetagamma subunits and CCG257284


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors.

Bouley, R.Waldschmidt, H.V.Cato, M.C.Cannavo, A.Song, J.Cheung, J.Y.Yao, X.Q.Koch, W.J.Larsen, S.D.Tesmer, J.J.G.

(2017) Mol. Pharmacol. 92: 707-717

  • DOI: 10.1124/mol.117.110130
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein-coupled receptor kinases (GRKs) phosphorylate activated receptors to promote arrestin binding, decoupling from heterotrimeric G proteins, and internalization. GRK2 and GRK5 are overexpressed in the failing heart and thus have become therape ...

    G protein-coupled receptor kinases (GRKs) phosphorylate activated receptors to promote arrestin binding, decoupling from heterotrimeric G proteins, and internalization. GRK2 and GRK5 are overexpressed in the failing heart and thus have become therapeutic targets. Previously, we discovered two classes of GRK2-selective inhibitors, one stemming from GSK180736A, a Rho-associated coiled-coil containing kinase 1 (ROCK1) inhibitor, the other from paroxetine, a selective serotonin-reuptake inhibitor. These two classes of compounds bind to the GRK2 active site in a similar configuration but contain different hinge-binding "warheads": indazole and benzodioxole, respectively. We surmised from our prior studies that an indazole would be the stronger hinge binder and would impart increased potency when substituted for benzodioxole in paroxetine derivatives. To test this hypothesis, we synthesized a series of hybrid compounds that allowed us to compare the effects of inhibitors that differ only in the identity of the warhead. The indazole-paroxetine analogs were indeed more potent than their respective benzodioxole derivatives but lost selectivity. To investigate how these two warheads dictate selectivity, we determined the crystal structures of three of the indazole hybrid compounds (CCG224061, CCG257284, and CCG258748) in complex with GRK2-Gβγ Comparison of these structures with those of analogous benzodioxole-containing complexes confirmed that the indazole-paroxetine hybrids form stronger interactions with the hinge of the kinase but also stabilize a distinct conformation of the kinase domain of GRK2 compared with previous complexes with paroxetine analogs. This conformation is analogous to one that can be assumed by GRK5, at least partially explaining the loss in selectivity.


    Organizational Affiliation

    Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-adrenergic receptor kinase 1
A
689Homo sapiensMutation(s): 0 
Gene Names: GRK2 (ADRBK1, BARK, BARK1)
EC: 2.7.11.15
Find proteins for P25098 (Homo sapiens)
Go to Gene View: GRK2
Go to UniProtKB:  P25098
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
340Bos taurusMutation(s): 0 
Gene Names: GNB1
Find proteins for P62871 (Bos taurus)
Go to Gene View: GNB1
Go to UniProtKB:  P62871
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
71Bos taurusMutation(s): 1 
Gene Names: GNG2
Find proteins for P63212 (Bos taurus)
Go to Gene View: GNG2
Go to UniProtKB:  P63212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AFV
Query on AFV

Download SDF File 
Download CCD File 
A
2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(pyridin-2-yl)methyl]benzamide
C26 H26 F N5 O2
QPWJXBKNAUGRGE-UGKGYDQZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.146α = 90.00
b = 241.443β = 90.00
c = 214.835γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release