5WG5

Human GRK2 in complex with Gbetagamma subunits and CCG224061


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1124/mol.117.110130
  • Primary Citation of Related Structures:  
    5WG3, 5WG4, 5WG5

  • 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 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-G βγ 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1689Homo sapiensMutation(s): 0 
Gene Names: GRK2ADRBK1BARKBARK1
EC: 2.7.11.15
UniProt & NIH Common Fund Data Resources
Find proteins for P25098 (Homo sapiens)
Explore P25098 
Go to UniProtKB:  P25098
PHAROS:  P25098
GTEx:  ENSG00000173020 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25098
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Bos taurusMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
Explore P62871 
Go to UniProtKB:  P62871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62871
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Bos taurusMutation(s): 1 
Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63212
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZSO (Subject of Investigation/LOI)
Query on ZSO

Download Ideal Coordinates CCD File 
D [auth A]5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-2H-indazole
C19 H20 F N3 O
ICFQMYOLILBYFP-YJBOKZPZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.022α = 90
b = 240.13β = 90
c = 211.611γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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: 2017-12-27
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description