8H7F | pdb_00008h7f

The crystal structure of human abl1 kinase domain in complex with abl1-B-EBA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8H7F

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases.

Chen, P.Tang, G.Zhu, C.Sun, J.Wang, X.Xiang, M.Huang, H.Wang, W.Li, L.Zhang, Z.M.Gao, L.Yao, S.Q.

(2023) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.2c11595
  • Primary Citation Related Structures: 
    8H7B, 8H7F, 8H7H

  • PubMed Abstract: 

    Lysine-targeting irreversible covalent inhibitors have attracted growing interests in recent years, especially in the fields of kinase research. Despite encouraging progress, few chemistries are available to develop inhibitors that are exclusively lysine-targeting, selective, and cell-active. We report herein a 2-ethynylbenzaldehyde (EBA)-based, lysine-targeting strategy to generate potent and selective small-molecule inhibitors of ABL kinase by selectively targeting the conserved catalytic lysine in the enzyme. We showed the resulting compounds were cell-active, capable of covalently engaging endogenous ABL kinase in K562 cells with long-residence time and few off-targets. We further validated the generality of this strategy by developing EBA-based irreversible inhibitors against EGFR (a kinase) and Mcl-1 (a nonkinase) that covalently reacted with the catalytic and noncatalytic lysine within each target.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.

Macromolecule Content 

  • Total Structure Weight: 64.91 kDa 
  • Atom Count: 4,441 
  • Modeled Residue Count: 524 
  • Deposited Residue Count: 554 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1
A, B
277Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
PHAROS:  P00519
GTEx:  ENSG00000097007 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QEW

Query on QEW



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1-[6-(6-methoxyisoquinolin-7-yl)-1,3-benzothiazol-2-yl]-3-(2-oxidanylideneethyl)urea
C20 H16 N4 O3 S
BTOGRSOLMDUWDV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.5018α = 90
b = 104.976β = 90
c = 132.487γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
xia2data scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary