5UKL | pdb_00005ukl

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 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5UKL

Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/acs.jmedchem.7b00112
  • Primary Citation Related Structures: 
    5UKK, 5UKL, 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 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
    • Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.

Macromolecule Content 

  • Total Structure Weight: 119.54 kDa 
  • Atom Count: 8,685 
  • Modeled Residue Count: 1,031 
  • Deposited Residue Count: 1,043 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1642Homo sapiensMutation(s): 1 
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1339Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]62Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIX

Query on SIX



Download:Ideal Coordinates CCD File
E [auth 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
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SIX BindingDB:  5UKL IC50: 630 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • 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
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description