3OT8

X-ray crystal structure of compound 17r bound to human Chk1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3OT8/pdb

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


• Deposited: 2010-09-10 Released: 2010-11-10 
• Deposition Author(s): Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.202 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach-Part 1.

Dwyer, M.P., Paruch, K., Labroli, M., Alvarez, C., Keertikar, K.M., Poker, C., Rossman, R., Fischmann, T.O., Duca, J.S., Madison, V., Parry, D., Davis, N., Seghezzi, W., Wiswell, D., Guzi, T.J.

(2011) Bioorg Med Chem Lett 21: 467-470

• PubMed: 21094608 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.113
• Primary Citation of Related Structures:  
  3OT8


• PubMed Abstract: 
  

  The synthesis and hit-to-lead SAR development of a pyrazolo[1,5-a]pyrimidine hit 4 is described leading to a series of potent, selective CHK1 inhibitors such as compound 17r. In the Letter, the further utility of the pyrazolo[1,5-a]pyrimidine template for the development of potent, selective kinase inhibitors is detailed.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, 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: 32.13 kDa 
• Atom Count: 2,318 
• Modelled Residue Count: 255 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	273	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MI5	B [auth A]	N-(3-methylisothiazol-5-yl)-3-(1-methyl-1H-pyrazol-4-yl)-5-[(3R)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidin-7-amine C19 H22 N8 S GZPYWHILDNLCNY-CYBMUJFWSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MI5	BindingDB:  3OT8	IC50: 9 (nM) from 1 assay(s)
	PDBBind:  3OT8	IC50: 9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.202 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.78	α = 90
b = 65.63	β = 94.78
c = 57.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Fischmann, T.O.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description