8FE9

Crystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 

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

Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk.

Kan, Y.Paung, Y.Kim, Y.Seeliger, M.A.Miller, W.T.

(2023) Biochemistry 62: 1124-1137

  • DOI: https://doi.org/10.1021/acs.biochem.2c00685
  • Primary Citation of Related Structures:  
    8FE9

  • PubMed Abstract: 

    Tyrosine kinases (TKs) play essential roles in signaling processes that regulate cell survival, migration, and proliferation. Dysregulation of tyrosine kinases underlies many disorders, including cancer, cardiovascular and developmental diseases, as well as pathologies of the immune system. Ack1 and Brk are nonreceptor tyrosine kinases (NRTKs) best known for their roles in cancer. Here, we have biochemically characterized novel Ack1 and Brk mutations identified in patients with systemic lupus erythematosus (SLE). These mutations are the first SLE-linked polymorphisms found among NRTKs. We show that two of the mutants are catalytically inactive, while the other three have reduced activity. To understand the structural changes associated with the loss-of-function phenotype, we solved the crystal structure of one of the Ack1 kinase mutants, K161Q. Furthermore, two of the mutated residues (Ack1 A156 and K161) critical for catalytic activity are highly conserved among other TKs, and their substitution in other members of the kinase family could have implications in cancer. In contrast to canonical gain-of-function mutations in TKs observed in many cancers, we report loss-of-function mutations in Ack1 and Brk, highlighting the complexity of TK involvement in human diseases.


  • Organizational Affiliation

    Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activated CDC42 kinase 1286Homo sapiensMutation(s): 1 
Gene Names: TNK2ACK1
EC: 2.7.10.2 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07912 (Homo sapiens)
Explore Q07912 
Go to UniProtKB:  Q07912
PHAROS:  Q07912
GTEx:  ENSG00000061938 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07912
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R9B (Subject of Investigation/LOI)
Query on R9B

Download Ideal Coordinates CCD File 
B [auth A]N-[(1S)-1-benzyl-2-[(6-chloro-2-oxo-1H-quinolin-4-yl)methylamino]-2-oxo-ethyl]-4-hydroxy-2-oxo-1H-quinoline-6-carbo
C29 H23 Cl N4 O5
DNDMLXSODUEUMP-DEOSSOPVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.69α = 90
b = 91.69β = 90
c = 190.066γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata processing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM119437
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI164424
Department of Veterans Affairs (VA, United States)United StatesBX002292

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release