2DS1

Human cyclin dependent kinase 2 complexed with the CDK4 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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

  • 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 m ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 2
A
298Homo sapiensMutation(s): 3 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1CD
Query on 1CD

Download SDF File 
Download CCD File 
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
5H,10H-17,19-(IMINOMETHANO)-4,6:9,12-DIMETHANODIBENZ[B,F][1,4,8,9,12]OXATETRAAZACYCLOPENTADECINE-20,23-DIONE,7,8,11,12-TETRAHYDRO-10-METHYL-,(10R,12S)
C22 H21 N5 O3
KBLPHMRCKHFBJB-OLZOCXBDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1CDIC50: 3.4 nM (98) BINDINGDB
1CDIC50: 6.4 nM BINDINGMOAD
1CDIC50: 3.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.050α = 90.00
b = 71.220β = 90.00
c = 53.580γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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