9BRH | pdb_00009brh

Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 in Complex with GRL056-21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AQ7 (Subject of Investigation/LOI)
Query on A1AQ7

Download Ideal Coordinates CCD File 
B [auth A](3Z)-N-[(1R)-1-(4-fluorophenyl)ethyl]-3-({4-[(furan-3-carbonyl)amino]-3,5-dimethyl-1H-pyrrol-2-yl}methylidene)-2-oxo-3,7-dihydro-2H-indole-5-carboxamide
C29 H25 F N4 O4
DTUOQJZFJLHXLS-GEWRUKCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.639α = 90
b = 138.639β = 90
c = 71.707γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing

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 Center for Research Resources (NIH/NCRR)United StatesCA023168

Revision History  (Full details and data files)

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