5UU1

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to BI-D1870


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.

Counago, R.M.Allerston, C.K.Savitsky, P.Azevedo, H.Godoi, P.H.Wells, C.I.Mascarello, A.de Souza Gama, F.H.Massirer, K.B.Zuercher, W.J.Guimaraes, C.R.W.Gileadi, O.

(2017) Sci Rep 7: 7501-7501

  • DOI: 10.1038/s41598-017-07755-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. However, understanding the cellular role of VRKs and e ...

    The human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. However, understanding the cellular role of VRKs and establishing their potential use as targets for therapeutic intervention has been limited by the lack of tool compounds that can specifically modulate the activity of these kinases in cells. Here we identified BI-D1870, a dihydropteridine inhibitor of RSK kinases, as a promising starting point for the development of chemical probes targeting the active VRKs. We solved co-crystal structures of both VRK1 and VRK2 bound to BI-D1870 and of VRK1 bound to two broad-spectrum inhibitors. These structures revealed that both VRKs can adopt a P-loop folded conformation, which is stabilized by different mechanisms on each protein. Based on these structures, we suggest modifications to the dihydropteridine scaffold that can be explored to produce potent and specific inhibitors towards VRK1 and VRK2.


    Organizational Affiliation

    Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP, Brazil. rafael.counago@unicamp.br.,Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil. rafael.counago@unicamp.br.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.,Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, Brazil.,Aché Laboratórios Farmacêuticos SA, Guarulhos, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase VRK2
A
324Homo sapiensMutation(s): 0 
Gene Names: VRK2
EC: 2.7.11.1
Find proteins for Q86Y07 (Homo sapiens)
Go to Gene View: VRK2
Go to UniProtKB:  Q86Y07
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7DZ
Query on 7DZ

Download SDF File 
Download CCD File 
A
(7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one
BI-D1870
C19 H23 F2 N5 O2
DTEKTGDVSARYDS-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.477α = 90.00
b = 72.683β = 90.00
c = 83.042γ = 90.00
Software Package:
Software NamePurpose
2016data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/50724-5

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Type: Author supporting evidence