Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 34.56 kDa 
• Atom Count: 2671 
• Residue Count: 292 
• Unique protein chains: 1

5OSM

Cdk2(F80C, C177A) with covalent adduct at C80

• DOI: 10.2210/pdb5OSM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-08-17 Released: 2018-03-14 
• Deposition Author(s): Craven, G., Morgan, R.M.L., Mann, D.J.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Cancer and Polio Research Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.206 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery.

Craven, G.B., Affron, D.P., Allen, C.E., Matthies, S., Greener, J.G., Morgan, R.M.L., Tate, E.W., Armstrong, A., Mann, D.J.

(2018) Angew Chem Int Ed Engl 57: 5257-5261

• PubMed: 29480525 
• DOI: 10.1002/anie.201711825
• Primary Citation of Related Structures:  
  5OO0, 5OSJ, 5OSM


• PubMed Abstract: 
  

Cysteine-reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high-quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan-reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine-reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2-selective allosteric (type IV) kinase inhibitor whose novel mode-of-action could be exploited therapeutically.

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Organizational Affiliation: 

Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	303	Homo sapiens	Mutation(s): 2  Gene Names: CDK2, CDKN2 EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AEQ	A	methyl 1-propanoyl-3,4-dihydro-2~{H}-quinoline-6-carboxylate C14 H17 N O3 BXTMIVXDDUNPOP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.206 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.713	α = 90
b = 71.218	β = 90
c = 72.317	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-08-17 
• Released Date: 2018-03-14 
Deposition Author(s): Craven, G., Morgan, R.M.L., Mann, D.J.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United States	EP/F500416/1
Cancer and Polio Research Fund	United Kingdom	--

Revision History 

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references