Cdk2(F80C, C177A) with covalent adduct at C80

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2303Homo sapiensMutation(s): 2 
Gene Names: CDK2CDKN2
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AEQ (Subject of Investigation/LOI)
Query on AEQ

Download Ideal Coordinates CCD File 
B [auth A]methyl 1-propanoyl-3,4-dihydro-2~{H}-quinoline-6-carboxylate
C14 H17 N O3
Experimental Data & Validation

Experimental Data

  • 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 = 52.713α = 90
b = 71.218β = 90
c = 72.317γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description