5UKM | pdb_00005ukm

bovine GRK2 in complex with human Gbetagamma subunits and CCG258208 (14as)

  • Classification: Transferase/Signaling Protein
  • Organism(s): Bos taurus, Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2017-01-23 Released: 2017-04-12 
  • Deposition Author(s): Cruz-Rodriguez, O., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and Michigan Technology Tri-Corridor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 
    0.252 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5UKM

Ligand Structure Quality Assessment 


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: 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: 127.59 kDa 
  • Atom Count: 8,246 
  • Modeled Residue Count: 1,020 
  • Deposited Residue Count: 1,116 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-adrenergic receptor kinase 1695Bos taurusMutation(s): 1 
Gene Names: GRK2ADRBK1
EC: 2.7.11.15
UniProt
Find proteins for P21146 (Bos taurus)
Explore P21146 
Go to UniProtKB:  P21146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21146
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-1350Homo 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]71Homo 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T0E

Query on T0E



Download:Ideal Coordinates CCD File
D [auth A]5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(1H-pyrazol-5-yl)methyl]benzamide
C24 H25 F N4 O4
XQUKEAYUAYTIBV-LPHOPBHVSA-N
CMT

Query on CMT



Download:Ideal Coordinates CCD File
F [auth G]O-METHYLCYSTEINE
C4 H9 N O2 S
MCYHPZGUONZRGO-VKHMYHEASA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
T0E BindingDB:  5UKM IC50: min: 30, max: 30 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free:  0.252 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.012α = 90
b = 74.15β = 115.46
c = 123.175γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008597
Michigan Economic Development Corporation and Michigan Technology Tri-CorridorUnited States085P1000817

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description