Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2643 
• Modelled Residue Count: 286 
• Deposited Residue Count: 322 
• Unique protein chains: 1

2YCF

Crystal Structure of Checkpoint Kinase 2 in complex with Inhibitor PV1531

• PDB DOI: 10.2210/pdb2YCF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-14 Released: 2011-11-16 
• Deposition Author(s): Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C.R., Pommier, Y., Shoemaker, R.H., Zhang, G., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Structural Characterization of Inhibitor Complexes with Checkpoint Kinase 2 (Chk2), a Drug Target for Cancer Therapy.

Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C.R., Zhang, G., Pommier, Y., Shoemaker, R.H., Waugh, D.S.

(2011) J Struct Biol 176: 292

• PubMed: 21963792 
• DOI: 10.1016/j.jsb.2011.09.008
• Primary Citation of Related Structures:  
  2XK9, 2YCF, 2YCQ, 2YCR, 2YCS


• PubMed Abstract: 
  

Chk2 (checkpoint kinase 2) is a serine/threonine kinase that participates in a series of signaling networks responsible for maintaining genomic integrity and responding to DNA damage. The development of selective Chk2 inhibitors has recently attracted much interest as a means of sensitizing cancer cells to current DNA-damaging agents used in the treatment of cancer. Additionally, selective Chk2 inhibitors may reduce p53-mediated apoptosis in normal tissues, thereby helping to mitigate adverse side effects from chemotherapy and radiation. Thus far, relatively few selective inhibitors of Chk2 have been described and none have yet progressed into clinical trials. Here, we report crystal structures of the catalytic domain of Chk2 in complex with a novel series of potent and selective small molecule inhibitors. These compounds exhibit nanomolar potencies and are selective for Chk2 over Chk1. The structures reported here elucidate the binding modes of these inhibitors to Chk2 and provide information that can be exploited for the structure-assisted design of novel chemotherapeutics.

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Organizational Affiliation: 

Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK2	A	322	Homo sapiens	Mutation(s): 0  Gene Names: CHEK2, CDS1, CHK2, RAD53 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96017 (Homo sapiens) Explore O96017  Go to UniProtKB:  O96017
PHAROS:  O96017 GTEx:  ENSG00000183765

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YCF	B [auth A]	(2E)-N-hydroxy-2-[1-(4-{[(4-{(1E)-1-[2-(N'-hydroxycarbamimidoyl)hydrazinylidene]ethyl}phenyl)carbamoyl]amino}phenyl)ethylidene]hydrazinecarboximidamide C19 H24 N10 O3 VVGIJVMXIRYKIO-DHSUVYDUSA-N
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YCF	PDBBind:  2YCF	IC50: 0.03 (nM) from 1 assay(s)
	Binding MOAD:  2YCF	IC50: 0.03 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.465	α = 90
b = 90.465	β = 90
c = 93.639	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-14 
• Released Date: 2011-11-16 
Deposition Author(s): Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C.R., Pommier, Y., Shoemaker, R.H., Zhang, G., Waugh, D.S.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release