9BRJ | pdb_00009brj

Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 in Complex with GRL093-22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.273 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Design, synthesis, and X-ray structural studies of a series of highly potent, selective, and drug-like G protein-coupled receptor kinase 5 inhibitors.

Ghosh, A.K.Chen, Y.Gadi, R.K.Sonawane, A.Gamage, S.P.Tesmer, J.G.

(2025) Eur J Med Chem 282: 117024-117024

  • DOI: https://doi.org/10.1016/j.ejmech.2024.117024
  • Primary Citation Related Structures: 
    9BRE, 9BRG, 9BRH, 9BRI, 9BRJ

  • PubMed Abstract: 

    G protein-coupled receptor kinase 5 (GRK5) has emerged as a potential drug development target against heart failure and cancer. A close homolog, GRK6 represents a therapeutic target for multiple myeloma. We have rationally designed a series of highly selective, potent, noncovalent, and drug-like GRK5 inhibitors. Several inhibitors exhibited low nanomolar GRK5 inhibition and high selectivity over GRK2, and, surprisingly, some were selective for GRK6. We determined high-resolution X-ray crystal structures of several inhibitors in complex with GRK5, which provide molecular insights into the ligand-binding site interactions responsible for GRK5 selectivity and potency.


  • Organizational Affiliation
    • Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA. Electronic address: akghosh@purdue.edu.

Macromolecule Content 

  • Total Structure Weight: 69.51 kDa 
  • Atom Count: 4,148 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 598 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G protein-coupled receptor kinase 5598Homo sapiensMutation(s): 1 
Gene Names: GRK5
EC: 2.7.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for P34947 (Homo sapiens)
Explore P34947 
Go to UniProtKB:  P34947
PHAROS:  P34947
GTEx:  ENSG00000198873 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34947
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AQ9
(Subject of Investigation/LOI)

Query on A1AQ9



Download:Ideal Coordinates CCD File
B [auth A](4S)-N-{5-[(Z)-(5-{[(1R)-1-(4-fluorophenyl)ethyl]carbamoyl}-2-oxo-2,7-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrol-3-yl}-2-methylimidazo[1,2-a]pyridine-3-carboxamide
C33 H29 F N6 O3
WTFJOTYVTOMVRC-NAHYFOQLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.273 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.475α = 90
b = 137.475β = 90
c = 70.766γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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 Center for Research Resources (NIH/NCRR)United StatesCA023168

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release