2YIR | pdb_00002yir

Structural analysis of checkpoint kinase 2 in complex with inhibitor PV1352

• PDB DOI: https://doi.org/10.2210/pdb2YIR/pdb

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


• Deposited: 2011-05-16 Released: 2011-09-07 
• Deposition Author(s): Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C., Zhang, G., Pommier, Y., Shoemaker, R.H., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.225 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structures of Checkpoint Kinase 2 in Complex with Inhibitors that Target its Gatekeeper-Dependent Hydrophobic Pocket.

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

(2011) FEBS Lett 585: 3245

• PubMed: 21907711 
• DOI: https://doi.org/10.1016/j.febslet.2011.08.050
• Primary Citation Related Structures: 
  2YIQ, 2YIR, 2YIT


• PubMed Abstract: 
  

  The serine/threonine checkpoint kinase 2 (Chk2) is an attractive molecular target for the development of small molecule inhibitors to treat cancer. Here, we report the rational design of Chk2 inhibitors that target the gatekeeper-dependent hydrophobic pocket located behind the adenine-binding region of the ATP-binding site. These compounds exhibit IC(50) values in the low nanomolar range and are highly selective for Chk2 over Chk1. X-ray crystallography was used to determine the structures of the inhibitors in complex with the catalytic kinase domain of Chk2 to verify their modes of binding.

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Organizational Affiliation: 
• Basic Science Program, SAIC-Frederick, Frederick, MD 21702-1201, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.03 kDa 
• Atom Count: 2,492 
• Modeled Residue Count: 286 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK2	A	323	Homo sapiens	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YIR	B [auth A]	(E)-N-(5-(2-CARBAMIMIDOYLHYDRAZONO)-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)-7-NITRO-1H-INDOLE-2-CARBOXAMIDE C20 H19 N7 O3 CFOWEKJDEFRRLQ-MFKUBSTISA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.225 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.243	α = 90
b = 91.243	β = 90
c = 93.466	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C., Zhang, G., Pommier, Y., Shoemaker, R.H., Waugh, D.S.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description