2DS1

Human cyclin dependent kinase 2 complexed with the CDK4 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-based drug design of a highly potent CDK1,2,4,6 inhibitor with novel macrocyclic quinoxalin-2-one structure

Kawanishi, N.Sugimoto, T.Shibata, J.Nakamura, K.Masutani, K.Ikuta, M.Hirai, H.

(2006) Bioorg Med Chem Lett 16: 5122-5126

  • DOI: 10.1016/j.bmcl.2006.07.026
  • Primary Citation of Related Structures:  
    2DS1

  • PubMed Abstract: 
  • The design of a novel series of cyclin-dependent kinase (CDK) inhibitors containing a macrocyclic quinoxaline-2-one is reported. Structure-based drug design and optimization from the starting point of diarylurea 2, which we previously reported as a moderate CDK1,2,4,6 inhibitor [J ...

    The design of a novel series of cyclin-dependent kinase (CDK) inhibitors containing a macrocyclic quinoxaline-2-one is reported. Structure-based drug design and optimization from the starting point of diarylurea 2, which we previously reported as a moderate CDK1,2,4,6 inhibitor [J. Biol.Chem.2001, 276, 27548], led to the discovery of potent CDK1,2,4,6 inhibitor that were suitable for iv administration for in vivo study.


    Organizational Affiliation

    Department of Medicinal Chemistry, Banyu Tsukuba Research Institute in collaboration with Merck Research Laboratories, Okubo-3, Tsukuba 300-2611, Ibaraki, Japan. nobuhiko_kawanishi@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A298Homo sapiensMutation(s): 3 
Gene Names: CDK2CDKN2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1CD (Subject of Investigation/LOI)
Query on 1CD

Download Ideal Coordinates CCD File 
B [auth A](13R,15S)-13-METHYL-16-OXA-8,9,12,22,24-PENTAAZAHEXACYCLO[15.6.2.16,9.1,12,15.0,2,7.0,21,25]HEPTACOSA-1(24),2,4,6,17(25 ),18,20-HEPTAENE-23,26-DIONE
C22 H21 N5 O3
KBLPHMRCKHFBJB-OLZOCXBDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1CD PDBBind:  2DS1 IC50: 3.4 (nM) from 1 assay(s)
Binding MOAD:  2DS1 IC50: 3.4 (nM) from 1 assay(s)
BindingDB:  2DS1 IC50: 3.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.05α = 90
b = 71.22β = 90
c = 53.58γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-06-17 
  • Released Date: 2007-06-19 
  • Deposition Author(s): Ikuta, M.

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance