2AYP | pdb_00002ayp

Crystal Structure of CHK1 with an Indol Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2AYP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-09-07 Released: 2006-09-12 
• Deposition Author(s): Lin, N.-H., Xia, P., Kovar, P., Chen, Z., Zhang, H., Rosenberg, S.H., Sham, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.314 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 

Literature

Synthesis and biological evaluation of 3-ethylidene-1,3-dihydro-indol-2-ones as novel checkpoint 1 inhibitors

Lin, N.-H., Xia, P., Kovar, P., Park, C., Chen, Z., Zhang, H., Rosenberg, S.H., Sham, H.L.

(2006) Bioorg Med Chem Lett 16: 421-426

• PubMed: 16242328 
• DOI: https://doi.org/10.1016/j.bmcl.2005.09.064
• Primary Citation of Related Structures:  
  2AYP


• PubMed Abstract: 
  

  Chk1 inhibitors have emerged as a novel class of neoplastic agents for abrogating the G2 DNA damage checkpoint arrest. Analogs of the Chk1 inhibitor, 3-ethylidene-1,3-dihydro-indol-2-one, were synthesized and tested in vitro for their inhibitory activities. The most promising compound identified from this series is analog 28, which possesses potent enzymatic and cellular activities.

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Organizational Affiliation: 

Cancer Research, R-47B, Global Pharmaceutical Products Division, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-3500, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.4 kDa 
• Atom Count: 2,201 
• Modeled Residue Count: 268 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	269	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
43A	B [auth A]	(3Z)-6-(4-HYDROXY-3-METHOXYPHENYL)-3-(1H-PYRROL-2-YLMETHYLENE)-1,3-DIHYDRO-2H-INDOL-2-ONE C20 H16 N2 O3 AYSXURJZVXBSRV-WJDWOHSUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
43A	BindingDB:  2AYP	Ki: 32 (nM) from 1 assay(s)
		IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.314 (Depositor) 
• R-Value Work:  0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.043	α = 90
b = 65.698	β = 94.39
c = 57.86	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-12 
Deposition Author(s): Lin, N.-H., Xia, P., Kovar, P., Chen, Z., Zhang, H., Rosenberg, S.H., Sham, H.L.

Revision History  

• Version 1.0: 2006-09-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations