Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 34.51 kDa 
• Atom Count: 2399 
• Modelled Residue Count: 269 
• Deposited Residue Count: 298 
• Unique protein chains: 1

4QYF

CHK1 kinase domain in complex with aminopyrazine compound 13

• PDB DOI: 10.2210/pdb4QYF/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-07-24 Released: 2014-12-17 
• Deposition Author(s): Appleton, B., Wu, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.223 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Discovery of the 1,7-diazacarbazole class of inhibitors of checkpoint kinase 1.

Gazzard, L., Appleton, B., Chapman, K., Chen, H., Clark, K., Drobnick, J., Goodacre, S., Halladay, J., Lyssikatos, J., Schmidt, S., Sideris, S., Wiesmann, C., Williams, K., Wu, P., Yen, I., Malek, S.

(2014) Bioorg Med Chem Lett 24: 5704-5709

• PubMed: 25453805 
• DOI: 10.1016/j.bmcl.2014.10.063
• Primary Citation of Related Structures:  
  4QYE, 4QYF, 4QYG, 4QYH


• PubMed Abstract: 
  

Checkpoint kinase 1 (ChK1) is activated in response to DNA damage, acting to temporarily block cell cycle progression and allow for DNA repair. It is envisaged that inhibition of ChK1 will sensitize tumor cells to treatment with DNA-damaging therapies, and may enhance the therapeutic window. High throughput screening identified carboxylate-containing diarylpyrazines as a prominent hit series, but with limited biochemical potency and no cellular activity. Through a series of SAR investigations and X-ray crystallographic analysis the critical role of polar contacts with conserved waters in the kinase back pocket was established. Structure-based design, guided by in silico modeling, transformed the series to better satisfy these contacts and the novel 1,7-diazacarbazole class of inhibitors was discovered. Here we present the genesis of this novel series and the identification of GNE-783, a potent, selective and orally bioavailable inhibitor of ChK1.

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Organizational Affiliation: 

Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	298	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3DV	B [auth A]	4-[3-amino-6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid C17 H13 N3 O3 SMCZWNHNLRIBBG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.223 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.971	α = 90
b = 65.948	β = 93.96
c = 58.118	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-24 
• Released Date: 2014-12-17 
Deposition Author(s): Appleton, B., Wu, P.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release