5OSJ

Cdk2(WT) with covalent adduct at C177


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1002/anie.201711825
  • Primary Citation of Related Structures:  

  • 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. Here ...

    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. Here we describe quantitative irreversible tethering (qIT), a general method for screening cysteine-reactive small molecules based upon the maximization of kinetic selectivity. We apply this method 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.


    Organizational Affiliation

    Imperial College London, South Kensington Campus, SW7 2AZ, London, UNITED KINGDOM.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
303Homo sapiensMutation(s): 0 
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
AAK
Query on AAK

Download SDF File 
Download CCD File 
A
~{tert}-butyl 4-propanoyl-2,3-dihydroquinoxaline-1-carboxylate
C16 H22 N2 O3
CNDTUXVSHRKQMX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.916α = 90.00
b = 71.111β = 90.00
c = 72.250γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/F500416/1
Cancer and Polio Research FundUnited Kingdom--

Revision History 

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