Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 31.66 kDa 
• Atom Count: 2362 
• Residue Count: 256 
• Unique protein chains: 1

3JVS

Characterization of the Chk1 allosteric inhibitor binding site

• DOI: 10.2210/pdb3JVS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-09-17 Released: 2009-10-06 
• Deposition Author(s): Chen, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.187 

Literature

Characterization of the CHK1 allosteric inhibitor binding site.

Vanderpool, D., Johnson, T.O., Ping, C., Bergqvist, S., Alton, G., Phonephaly, S., Rui, E., Luo, C., Deng, Y.L., Grant, S., Quenzer, T., Margosiak, S., Register, J., Brown, E., Ermolieff, J.

(2009) Biochemistry 48: 9823-9830

• PubMed: 19743875 
• DOI: 10.1021/bi900258v
• Primary Citation of Related Structures:  
  3JVR, 3JVS


• PubMed Abstract: 
  

Checkpoint kinase 1 (CHK1) is a key element in the DNA damage response pathway and plays a crucial role in the S-G(2)-phase checkpoint. Inhibiting CHK1 is a therapeutic strategy involving abrogation of the G2/M mitotic checkpoint defense of tumor cells toward lethal damage induced by DNA-directed chemotherapeutic agents. To date, most CHK1 inhibition approaches have involved targeting the ATP site of this kinase. In this study, we provide crystallographic and kinetic characterization of two small molecule inhibitors that bind to an allosteric site in the proximity of the CHK1 substrate site. Analysis of kinetic and biophysical data has led to the conclusion that these small molecule allosteric site inhibitors of CHK1 are reversible and are neither ATP- nor peptide substrate-competitive. K(i) values of 1.89 and 0.15 microM, respectively, have been determined for these compounds using a mixed inhibitor kinetic analysis. Cocrystal structures of the inhibitors bound to CHK1 reveal an allosteric site, unique to CHK1, located in the C-terminal domain and consisting of a shallow groove linked to a small hydrophobic pocket. The pocket displays induced fit characteristics in the presence of the two inhibitors. These findings establish the potential for the development of highly selective CHK1 inhibitors.

---

Organizational Affiliation: 

Department of Biochemistry and Primary Screening, Pfizer, La Jolla, San Diego 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	271	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGY	A	2-[(4-tert-butyl-3-nitrophenyl)carbonyl]-N-naphthalen-1-ylhydrazinecarboxamide C22 H22 N4 O4 YZMKNNITNHTADN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AGY	Ki:  146   nM  Binding MOAD
AGY	Kd :  290   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.754	α = 90
b = 65.578	β = 93.73
c = 57.931	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-17 
• Released Date: 2009-10-06 
Deposition Author(s): Chen, P.

Revision History 

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-07
  Changes: Source and taxonomy