4HYH | pdb_00004hyh

X-RAY Crystal structure of compound 39 bound to human chk1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb4HYH/pdb

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


• Deposited: 2012-11-13 Released: 2013-03-06 
• Deposition Author(s): Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors.

Huang, X., Cheng, C.C., Fischmann, T.O., Duca, J.S., Richards, M., Tadikonda, P.K., Reddy, P.A., Zhao, L., Arshad Siddiqui, M., Parry, D., Davis, N., Seghezzi, W., Wiswell, D., Shipps, G.W.

(2013) Bioorg Med Chem Lett 23: 2590-2594

• PubMed: 23535330 
• DOI: https://doi.org/10.1016/j.bmcl.2013.02.108
• Primary Citation Related Structures: 
  4HYH, 4HYI


• PubMed Abstract: 
  

  Drug design efforts in the emerging 2-aminothiazole-4-carboxamide class of CHK1 inhibitors have uncovered specific combinations of key substructures within the molecule; resulting in significant improvements in cell-based activity while retaining a greater than one hundred-fold selectivity against CDK2. The X-ray crystal structure of a complex between compound 39 and the CHK1 protein detailing a 'U-shaped' topology and key interactions with the protein surface at the ATP site is also reported.

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Organizational Affiliation: 
• Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.49 kDa 
• Atom Count: 2,297 
• Modeled Residue Count: 263 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	289	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 GTEx:  ENSG00000149554

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1AM	B [auth A]	2-(6-methoxy-1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-[4-(piperazin-1-yl)pyridin-3-yl]-1,3-thiazole-4-carboxamide C22 H22 N6 O3 S KLJVDMAOKMSBQX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1AM	BindingDB:  4HYH	IC50: min: 1, max: 3.7 (nM) from 2 assay(s)
		EC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.97	α = 90
b = 65.96	β = 102.39
c = 54.42	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Fischmann, T.O.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations