4WBO | pdb_00004wbo

Bovine G Protein Coupled Receptor Kinase 1 in Complex with Amlexanox

  • Classification: TRANSFERASE/TRANSFERASE INHIBITOR
  • Organism(s): Bos taurus
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2014-09-03 Released: 2014-11-05 
  • Deposition Author(s): 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, National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4WBO

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification and characterization of amlexanox as a g protein-coupled receptor kinase 5 inhibitor.

Homan, K.T.Wu, E.Cannavo, A.Koch, W.J.Tesmer, J.J.

(2014) Molecules 19: 16937-16949

  • DOI: https://doi.org/10.3390/molecules191016937
  • Primary Citation Related Structures: 
    4WBO

  • PubMed Abstract: 

    G protein-coupled receptor kinases (GRKs) have been implicated in human diseases ranging from heart failure to diabetes. Previous studies have identified several compounds that selectively inhibit GRK2, such as paroxetine and balanol. Far fewer selective inhibitors have been reported for GRK5, a target for the treatment of cardiac hypertrophy, and the mechanism of action of reported compounds is unknown. To identify novel scaffolds that selectively inhibit GRK5, a differential scanning fluorometry screen was used to probe a library of 4480 compounds. The best hit was amlexanox, an FDA-approved anti-inflammatory, anti-allergic immunomodulator. The crystal structure of amlexanox in complex with GRK1 demonstrates that its tricyclic aromatic ring system forms ATP-like interactions with the hinge of the kinase domain, which is likely similar to how this drug binds to IκB kinase ε (IKKε), another kinase known to be inhibited by this compound. Amlexanox was also able to inhibit myocyte enhancer factor 2 transcriptional activity in neonatal rat ventricular myocytes in a manner consistent with GRK5 inhibition. The GRK1 amlexanox structure thus serves as a springboard for the rational design of inhibitors with improved potency and selectivity for GRK5 and IKKε.


  • Organizational Affiliation
    • Life Sciences Institute and the Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecule Content 

  • Total Structure Weight: 246.2 kDa 
  • Atom Count: 15,932 
  • Modeled Residue Count: 1,964 
  • Deposited Residue Count: 2,164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhodopsin kinase
A, B, C, D
541Bos taurusMutation(s): 0 
Gene Names: GRK1RHOK
EC: 2.7.11.14
UniProt
Find proteins for P28327 (Bos taurus)
Explore P28327 
Go to UniProtKB:  P28327
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28327
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on ANW



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
2-amino-7-(1-methylethyl)-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid
C16 H14 N2 O4
SGRYPYWGNKJSDL-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.112α = 90
b = 119.166β = 90
c = 174.261γ = 90
Software Package:
Software NamePurpose
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, HL086865
American Heart AssociationUnited StatesN014938
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesP60DK020572

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Refinement description