2DS1

Human cyclin dependent kinase 2 complexed with the CDK4 inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb2DS1/pdb

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


• 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: 2.00 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: https://doi.org/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. 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]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.33 kDa 
• Atom Count: 2,501 
• Modelled Residue Count: 290 
• 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): 3  Gene Names: CDK2, CDKN2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1CD	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

Binding Affinity Annotations
ID	Source	Binding Affinity
1CD	PDBBind:  2DS1	IC50: 3.4 (nM) from 1 assay(s)
	BindingDB:  2DS1	IC50: 3.4 (nM) from 1 assay(s)
	Binding MOAD:  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 = 72.05	α = 90
b = 71.22	β = 90
c = 53.58	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description