Human vaccinia-related kinase 1

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1038/s41598-017-07755-y
  • Primary Citation of Related Structures:  
    3OP5, 5UKF, 5UU1, 5UVF

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VRK1
A, B, C, D
364Homo sapiensMutation(s): 11 
Gene Names: VRK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99986 (Homo sapiens)
Explore Q99986 
Go to UniProtKB:  Q99986
PHAROS:  Q99986
GTEx:  ENSG00000100749 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99986
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on REB

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
O [auth D]
C18 H17 N7
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
M [auth C],
N [auth C]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.97α = 90
b = 97.19β = 90
c = 191.99γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-08-29
    Changes: Structure summary
  • Version 1.3: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description