2YWP | pdb_00002ywp

Crystal Structure of CHK1 with a Urea Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2YWP/pdb
• Entry: 2YWP supersedes: 2FGA

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-21 Released: 2007-05-08 
• Deposition Author(s): Park, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Synthesis and biological evaluation of 1-(2,4,5-trisubstituted phenyl)-3-(5-cyanopyrazin-2-yl)ureas as potent Chk1 kinase inhibitors

Li, G., Hasvold, L.A., Tao, Z.-F., Wang, G.T., Gwaltney II, S.L., Patel, J., Kovar, P., Credo, R.B., Chen, Z., Zhang, H., Park, C., Sham, H.L., Sowin, T., Rosenberg, S.H., Lin, N.-H.

(2006) Bioorg Med Chem Lett 16: 2293-2298

• PubMed: 16446090 
• DOI: https://doi.org/10.1016/j.bmcl.2006.01.028
• Primary Citation of Related Structures:  
  2YWP


• PubMed Abstract: 
  

  Based on the X-ray crystallography of our lead compound 1-(5-chloro-2,4-dimethoxyphenyl)-3-(5-cyanopyrazin-2-yl)urea in the checkpoint kinase 1 (Chk1) enzyme, we modified R4, and to a lesser extent, R2, and R5 of the phenyl ring, and made a variety of N-aryl-N'-pyrazinylurea Chk1 inhibitors. Enzymatic activity less than 20 nM was observed in 15 of 41 compounds. Compound 8i provided the best overall results in the cellular assays as it abrogated doxorubicin-induced cell cycle arrest (IC50=1.7 microM) and enhanced doxorubicin cytotoxicity (IC50=0.44 microM) while displaying no single agent activity.

---

Organizational Affiliation: 

Cancer Research, Global Pharmaceutical Research & Development, Abbott Laboratories, Abbott Park, IL 60064, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.4 kDa 
• Atom Count: 2,208 
• Modelled Residue Count: 269 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	269	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A42	B [auth A]	1-(5-CHLORO-2,4-DIMETHOXYPHENYL)-3-(5-CYANOPYRAZIN-2-YL)UREA C14 H12 Cl N5 O3 URQYPXQXSVUVRG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A42	BindingDB:  2YWP	Ki: 10 (nM) from 1 assay(s)
		IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.863	α = 90
b = 65.513	β = 94.07
c = 57.84	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Park, C.
• This entry supersedes: 2FGA

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations