Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34328.79 
• Atom Count: 2361 
• Residue Count: 298 
• Unique protein chains: 1

2DS1

Human cyclin dependent kinase 2 complexed with the CDK4 inhibitor

• DOI: 10.2210/pdb2DS1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.290 
• R-Value Work: 0.225 

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

• PubMed: 16876403 
• 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 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Banyu Tsukuba Research Institute in collaboration with Merck Research Laboratories, Okubo-3, Tsukuba 300-2611, Ibaraki, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1CD	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1CD	IC50: 3.4 nM (98) BINDINGDB
1CD	IC50: 6.4 nM BINDINGMOAD
1CD	IC50: 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 = 72.050	α = 90.00
b = 71.220	β = 90.00
c = 53.580	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CNS	refinement
AMoRE	phasing

Structure Validation

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