5UKL

Human GRK2 in complex with Gbetagamma subunits and CCG222886 (14bd)

  • Classification: TRANSFERASE/TRANSFERASE INHIBITOR
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2017-01-23 Released: 2017-04-05 
  • Deposition Author(s): Cato, M.C., Homan, K.T., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Heart Association, Center for Discovery of New Medicine, University of Michigan, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and Michigan Technology Tri-Corridor Grant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-Based Design of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors Based on Paroxetine.

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

(2017) J Med Chem 60: 3052-3069

  • DOI: 10.1021/acs.jmedchem.7b00112
  • Primary Citation of Related Structures:  
    5UKL, 5UKK, 5UKM

  • PubMed Abstract: 
  • In heart failure, the β-adrenergic receptors (βARs) become desensitized and uncoupled from heterotrimeric G proteins. This process is initiated by G protein-coupled receptor kinases (GRKs), some of which are upregulated in the failing heart, making t ...

    In heart failure, the β-adrenergic receptors (βARs) become desensitized and uncoupled from heterotrimeric G proteins. This process is initiated by G protein-coupled receptor kinases (GRKs), some of which are upregulated in the failing heart, making them desirable therapeutic targets. The selective serotonin reuptake inhibitor, paroxetine, was previously identified as a GRK2 inhibitor. Utilizing a structure-based drug design approach, we modified paroxetine to generate a small compound library. Included in this series is a highly potent and selective GRK2 inhibitor, 14as, with an IC 50 of 30 nM against GRK2 and greater than 230-fold selectivity over other GRKs and kinases. Furthermore, 14as showed a 100-fold improvement in cardiomyocyte contractility assays over paroxetine and a plasma concentration higher than its IC 50 for over 7 h. Three of these inhibitors, including 14as, were additionally crystallized in complex with GRK2 to give insights into the structural determinants of potency and selectivity of these inhibitors.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1A642Homo sapiensMutation(s): 1 
Gene Names: GRK2ADRBK1BARKBARK1
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B339Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2G62Homo sapiensMutation(s): 0 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIX
Query on SIX

Download Ideal Coordinates CCD File 
A
2-{5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluorophenyl}-N-[2-(1H-pyrazol-4-yl)ethyl]acetamide
C26 H29 F N4 O4
UWGQNVKEQMCXMS-UNMCSNQZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SIXIC50:  630   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.255α = 90
b = 71.429β = 110.51
c = 111.259γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

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
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL122416
American Heart AssociationUnited StatesN014938
American Heart AssociationUnited States15PRE22730028
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR37 HL061690
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01 HL075443
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01 HL108806
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01 HL091799
Center for Discovery of New Medicine, University of MichiganUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008597
Michigan Economic Development Corporation and Michigan Technology Tri-Corridor GrantUnited States085P1000817

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2017-09-27
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence, Derived calculations