3LE6

The structure of cyclin dependent kinase 2 (CKD2) with a pyrazolobenzodiazepine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LE6/pdb

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


• Deposited: 2010-01-14 Released: 2010-11-17 
• Deposition Author(s): Lukacs, C.M., Swain, A., Crowther, R.L., Kammlott, R.U., Liu, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Pyrazolobenzodiazepines: part I. Synthesis and SAR of a potent class of kinase inhibitors.

Liu, J.J., Daniewski, I., Ding, Q., Higgins, B., Ju, G., Kolinsky, K., Konzelmann, F., Lukacs, C., Pizzolato, G., Rossman, P., Swain, A., Thakkar, K., Wei, C.C., Miklowski, D., Yang, H., Yin, X., Wovkulich, P.M.

(2010) Bioorg Med Chem Lett 20: 5984-5987

• PubMed: 20832307 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.079
• Primary Citation of Related Structures:  
  3LE6


• PubMed Abstract: 
  

  A novel series of pyrazolobenzodiazepines 3 has been identified as potent inhibitors of cyclin-dependent kinase 2 (CDK2). Their synthesis and structure-activity relationships (SAR) are described. Representative compounds from this class reversibly inhibit CDK2 activity in vitro, and block cell cycle progression in human tumor cell lines. Further exploration has revealed that this class of compounds inhibits several kinases that play critical roles in cancer cell growth and division as well as tumor angiogenesis. Together, these properties suggest a compelling basis for their use as antitumor agents.

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Organizational Affiliation: 

Discovery Chemistry, Hoffmann-La Roche Inc., Nutley, NJ 07110, 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: 34.33 kDa 
• Atom Count: 2,501 
• Modelled Residue Count: 283 
• 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  Gene Names: CDK2 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
2BZ	B [auth A]	5-(2-chlorophenyl)-3-methyl-7-nitropyrazolo[3,4-b][1,4]benzodiazepine C17 H10 Cl N5 O2 NKUOWCWVEBHJCR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2BZ	PDBBind:  3LE6	IC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.22	α = 90
b = 70.964	β = 90
c = 72.211	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Lukacs, C.M., Swain, A., Crowther, R.L., Kammlott, R.U., Liu, J.J.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations