2R64

Crystal structure of a 3-aminoindazole compound with CDK2

• PDB DOI: https://doi.org/10.2210/pdb2R64/pdb

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


• Deposited: 2007-09-05 Released: 2008-09-09 
• Deposition Author(s): Lee, J., Choi, H., Kim, K.H., Jeong, S., Park, J.W., Baek, C.S., Lee, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Synthesis and biological evaluation of 3,5-diaminoindazoles as cyclin-dependent kinase inhibitors.

Lee, J., Choi, H., Kim, K.H., Jeong, S., Park, J.W., Baek, C.S., Lee, S.H.

(2008) Bioorg Med Chem Lett 18: 2292-2295

• PubMed: 18353638 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.002
• Primary Citation of Related Structures:  
  2R64


• PubMed Abstract: 
  

  A novel series of 3,5-diaminoindazoles were prepared and found to be CDK inhibitors. Potent inhibitors against CDK1 and CDK2 were obtained by introduction of 1lambda(6)-isothiazolidine-1,1-dioxide at 5-position of indazole. Anti-proliferative activities of compounds were evaluated using EJ, HCT116, SW620, and A549 cancer cell lines.

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Organizational Affiliation: 

Department of Chemistry, Keimyung University, 1000 Sindang-Dong, Dalseo-Gu, Daegu 704-701, South Korea. [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: 34.43 kDa 
• Atom Count: 2,349 
• Modelled Residue Count: 279 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
740	B [auth A]	N-[5-(1,1-DIOXIDOISOTHIAZOLIDIN-2-YL)-1H-INDAZOL-3-YL]-2-(4-PIPERIDIN-1-YLPHENYL)ACETAMIDE C23 H27 N5 O3 S ZXYIRNXOAJYLCU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
740	BindingDB:  2R64	IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.449	α = 90
b = 71.279	β = 90
c = 71.985	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Lee, J., Choi, H., Kim, K.H., Jeong, S., Park, J.W., Baek, C.S., Lee, S.H.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations