9BRF | pdb_00009brf

Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 in Complex with GRL004-21

• PDB DOI: https://doi.org/10.2210/pdb9BRF/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-11 Released: 2025-05-14 
• Deposition Author(s): Chen, Y., Tesmer, J.J.G.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.277 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structural insights into a class of GRK5 inhibitors

Chen, Y., Tesmer, J.J.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.46 kDa 
• Atom Count: 4,145 
• Modeled Residue Count: 503 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein-coupled receptor kinase 5	A	598	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AQ5 (Subject of Investigation/LOI)	B [auth A]	(3Z)-3-{[3,5-dimethyl-4-(2-oxo-2-phenylacetamido)-1H-pyrrol-2-yl]methylidene}-2-oxo-N-[(1R)-1-phenylethyl]-3,7-dihydro-2H-indole-5-carboxamide C32 H28 N4 O4 LYBBCQSHMUMOJF-DWGAWOTKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.014	α = 90
b = 138.014	β = 90
c = 71.145	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Chen, Y., Tesmer, J.J.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL071818
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	CA023168

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release