5HE3

Bovine GRK2 in complex with Gbetagamma subunits and CCG224411


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Design, Synthesis, and Biological Evaluation of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors.

Waldschmidt, H.V.Homan, K.T.Cruz-Rodriguez, O.Cato, M.C.Waninger-Saroni, J.Larimore, K.M.Cannavo, A.Song, J.Cheung, J.Y.Kirchhoff, P.D.Koch, W.J.Tesmer, J.J.Larsen, S.D.

(2016) J Med Chem 59: 3793-3807

  • DOI: 10.1021/acs.jmedchem.5b02000
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCRs) are central to many physiological processes. Regulation of this superfamily of receptors is controlled by GPCR kinases (GRKs), some of which have been implicated in heart failure. GSK180736A, developed as a Rho-ass ...

    G protein-coupled receptors (GPCRs) are central to many physiological processes. Regulation of this superfamily of receptors is controlled by GPCR kinases (GRKs), some of which have been implicated in heart failure. GSK180736A, developed as a Rho-associated coiled-coil kinase 1 (ROCK1) inhibitor, was identified as an inhibitor of GRK2 and co-crystallized in the active site. Guided by its binding pose overlaid with the binding pose of a known potent GRK2 inhibitor, Takeda103A, a library of hybrid inhibitors was developed. This campaign produced several compounds possessing high potency and selectivity for GRK2 over other GRK subfamilies, PKA, and ROCK1. The most selective compound, 12n (CCG-224406), had an IC50 for GRK2 of 130 nM, >700-fold selectivity over other GRK subfamilies, and no detectable inhibition of ROCK1. Four of the new inhibitors were crystallized with GRK2 to give molecular insights into the binding and kinase selectivity of this class of inhibitors.


    Organizational Affiliation

    Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-adrenergic receptor kinase 1
A
641Bos taurusMutation(s): 0 
Gene Names: ADRBK1GRK2
EC: 2.7.11.15
Find proteins for P21146 (Bos taurus)
Go to UniProtKB:  P21146

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
339Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Go to UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FF1
Query on FF1

Download CCD File 
A
(4~{S})-4-[3-[2-(2,6-dimethylphenyl)ethylcarbamoyl]-4-fluoranyl-phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide
C30 H29 F N6 O3
QTCMCOOGSCOKGD-MHZLTWQESA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FF1IC50:  230   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.031α = 90
b = 239.412β = 90
c = 208.625γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL071818
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL086865
American Heart AssociationUnited StatesN014938
American Heart AssociationUnited States15PRE22730028
Michigan Economic Development Corporation and Michigan Technology Tri-Corridor GrantUnited States085P1000817

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence