Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129.54 kDa 
• Atom Count: 9513 
• Modelled Residue Count: 1110 
• Deposited Residue Count: 1126 
• Unique protein chains: 2

5CYI

CDK2/Cyclin A covalent complex with 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300)

• DOI: 10.2210/pdb5CYI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-30 Released: 2015-09-16 
• Deposition Author(s): Anscombe, E., Meschini, E., Vidal, R.M., Martin, M.P., Staunton, D., Geitmann, M., Danielson, U.H., Stanley, W.A., Wang, L.Z., Reuillon, T., Golding, B.T., Cano, C., Newell, D.R., Noble, M.E.M., Wedge, S.R., Endicott, J.A., Griffin, R.J.
• Funding Organization(s): Medical Research Council (United Kingdom), Cancer Research UK, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Identification and Characterization of an Irreversible Inhibitor of CDK2.

Anscombe, E., Meschini, E., Mora-Vidal, R., Martin, M.P., Staunton, D., Geitmann, M., Danielson, U.H., Stanley, W.A., Wang, L.Z., Reuillon, T., Golding, B.T., Cano, C., Newell, D.R., Noble, M.E., Wedge, S.R., Endicott, J.A., Griffin, R.J.

(2015) Chem Biol 22: 1159-1164

• PubMed: 26320860 
• DOI: 10.1016/j.chembiol.2015.07.018
• Primary Citation of Related Structures:  
  5CYI


• PubMed Abstract: 
  

Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.

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Organizational Affiliation: 

Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A, C	303	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B, D	260	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
55S (Subject of Investigation/LOI)	E [auth A], F [auth C]	6-(cyclohexylmethoxy)-N-[4-(ethylsulfonyl)phenyl]-9H-purin-2-amine C20 H25 N5 O3 S SIKZOJIFMBUYSK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.286	α = 90
b = 135.289	β = 90
c = 148.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-07-30 
• Released Date: 2015-09-16 
Deposition Author(s): Anscombe, E., Meschini, E., Vidal, R.M., Martin, M.P., Staunton, D., Geitmann, M., Danielson, U.H., Stanley, W.A., Wang, L.Z., Reuillon, T., Golding, B.T., Cano, C., Newell, D.R., Noble, M.E.M., Wedge, S.R., Endicott, J.A., Griffin, R.J.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G0901526
Cancer Research UK	United Kingdom	C240/A15751
European Union	United Kingdom	FP6-PROKINASE

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence