3PVW

Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD103A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors.

Thal, D.M.Yeow, R.Y.Schoenau, C.Huber, J.Tesmer, J.J.

(2011) Mol.Pharmacol. 80: 294-303

  • DOI: 10.1124/mol.111.071522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by G ...

    G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-Gβγ complex in the presence of two of these inhibitors. Comparison with the apoGRK2-Gβγ structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Room 3425, Ann Arbor, MI 48109, USA. tesmerjj@umich.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-adrenergic receptor kinase 1
A
695Bos taurusMutation(s): 1 
Gene Names: GRK2 (ADRBK1)
EC: 2.7.11.15
Find proteins for P21146 (Bos taurus)
Go to Gene View: GRK2
Go to UniProtKB:  P21146
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
74Bos taurusMutation(s): 0 
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
QRX
Query on QRX

Download SDF File 
Download CCD File 
A
N-(2,6-difluorobenzyl)-3-({[4-propyl-5-(pyrimidin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide
C24 H23 F2 N7 O
VWBSMGFTNCQOMB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMT
Query on CMT
G
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QRXIC50: 54 nM BINDINGMOAD
QRXIC50: 54 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 187.564α = 90.00
b = 74.227β = 115.65
c = 123.346γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
SCALEPACKdata scaling
REFMACphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references