3OT3

X-ray crystal structure of compound 22k bound to human Chk1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3OT3/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: 1.44 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach-Part 2.

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

(2011) Bioorg Med Chem Lett 21: 471-474

• PubMed: 21094607 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.114
• Primary Citation of Related Structures:  
  3OT3


• PubMed Abstract: 
  

  Previous efforts by our group have established pyrazolo[1,5-a]pyrimidine as a viable core for the development of potent and selective CDK inhibitors. As part of an effort to utilize the pyrazolo[1,5-a]pyrimidine core as a template for the design and synthesis of potent and selective kinase inhibitors, we focused on a key regulator in the cell cycle progression, CHK1. Continued SAR development of the pyrazolo[1,5-a]pyrimidine core at the C5 and C6 positions, in conjunction with previously disclosed SAR at the C3 and C7 positions, led to the discovery of potent and selective CHK1 inhibitors.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States. [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: 31.85 kDa 
• Atom Count: 2,446 
• Modelled Residue Count: 261 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
22K	B [auth A]	5-[(1R,3S)-3-aminocyclohexyl]-6-bromo-3-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-7-amine C16 H20 Br N7 CKLKHZYNDIKOOE-KOLCDFICSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
22K	PDBBind:  3OT3	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.83	α = 90
b = 65.78	β = 94.41
c = 57.72	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	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