Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2342 
• Modelled Residue Count: 265 
• Deposited Residue Count: 297 
• Unique protein chains: 1

2CGX

Identification of chemically diverse Chk1 inhibitors by receptor- based virtual screening

• DOI: 10.2210/pdb2CGX/pdb

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


• Deposited: 2006-03-09 Released: 2006-04-05 
• Deposition Author(s): Foloppe, N., Fisher, L.M., Howes, R., Potter, A., Robertson, A.G.S., Surgenor, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Identification of Chemically Diverse Chk1 Inhibitors by Receptor-Based Virtual Screening.

Foloppe, N., Fisher, L.M., Howes, R., Potter, A., Robertson, A.G.S., Surgenor, A.E.

(2006) Bioorg Med Chem 14: 4792

• PubMed: 16574416 
• DOI: 10.1016/j.bmc.2006.03.021
• Primary Citation of Related Structures:  
  2CGU, 2CGV, 2CGW, 2CGX


• PubMed Abstract: 
  

Inhibition of the Chk1 kinase by small molecules is of great therapeutic interest for oncology and in understanding the cellular regulation of the G2/M checkpoint. We report how computational docking of a large electronic catalogue of compounds to an X-ray structure of the Chk1 ATP-binding site allowed prioritisation of a small subset of these compounds for assay. This led to the discovery of 10 novel Chk1 inhibitors, distributed among nine new and clearly different chemical scaffolds. Several of these scaffolds have promising lead-like properties. All these ligands act by competitive binding to the targeted ATP site. The crystal structures of four of these compounds bound to this site are presented, and reasonable modelled docking modes are suggested for the 5 other scaffolds. This structural context is used to assess the potential of these scaffolds for further medicinal chemistry efforts, suggesting that several of them could be elaborated to make additional interactions with the buried part of the ATP site. Some unusual interactions with the conserved kinase backbone motif are pointed out. The ligand-binding modes are also used to discuss their medicinal chemistry potential with respect to undesirable chemical functionalities, whether these functionalities bind directly to the protein or not. Overall, this work illustrates how virtual screening can identify a diverse set of ligands which bind to the targeted site. The structural models for these ligands in the Chk1 ATP-binding site will facilitate further medicinal chemistry efforts targeting this kinase.

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Organizational Affiliation: 

Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK1	A	297	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
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
3D3 (Subject of Investigation/LOI)	B [auth A]	2-[(6-AMINO-7H-PURIN-8-YL)THIO]ACETAMIDE C7 H8 N6 O S LZGZHYMVMFIEIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3D3	BindingDB:  2CGX	IC50: 1.56e+4 (nM) from 1 assay(s)
	PDBBind:  2CGX	IC50: 1.56e+4 (nM) from 1 assay(s)
	Binding MOAD:  2CGX	IC50: 1.56e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.957	α = 90
b = 65.78	β = 102.46
c = 54.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-03-09 
• Released Date: 2006-04-05 
Deposition Author(s): Foloppe, N., Fisher, L.M., Howes, R., Potter, A., Robertson, A.G.S., Surgenor, A.E.

Revision History  

• Version 1.0: 2006-04-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance