5FP6

Structure of cyclin-dependent kinase 2 with small-molecule ligand 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (AT17833) in an alternate binding site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Detection of Secondary Binding Sites in Proteins Using Fragment Screening.

Ludlow, R.F.Verdonk, M.L.Saini, H.K.Tickle, I.J.Jhoti, H.

(2015) Proc Natl Acad Sci U S A 112: 15910

  • DOI: 10.1073/pnas.1518946112
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins ...

    Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.


    Related Citations: 
    • Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design.
      Wyatt, P.G., Woodhead, A.J., Berdini, V., Boulstridge, J.A., Carr, M.G., Cross, D.M., Davis, D.J., Devine, L.A., Early, T.R., Feltell, R.E., Lewis, E.J., Mcmenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Reule, M., Saxty, G., Seavers, L.C.A., Smith, D., Squires, M.S., Trewartha, G., Walker, M.T., Woolford, A.J.
      (2008) J Med Chem 51: 4986

    Organizational Affiliation

    Astex Pharmaceuticals, Cambridge CB4 0QA, United Kingdom harren.jhoti@astx.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 2
A
298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MFZ
Query on MFZ

Download CCD File 
A
3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol
C11 H7 Cl2 N O
VIZAOCOKGQUJRZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.917α = 90
b = 72.214β = 90
c = 72.198γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
DTSCALEdata scaling
CSEARCHphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references