5UKF

Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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 and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VRK1A, B, C, D363Homo sapiensMutation(s): 11 
Gene Names: VRK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99986 (Homo sapiens)
Explore Q99986 
Go to UniProtKB:  Q99986
PHAROS:  Q99986
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8E1 (Subject of Investigation/LOI)
Query on 8E1

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], N [auth C], S [auth D]4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide
C16 H12 N4 O3 S2
LTYGAJVXAFJKSY-XFFZJAGNSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
R [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], M [auth B], Q [auth C], T [auth D], U [auth D], V [auth D], W [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.138α = 90
b = 96.051β = 90
c = 192.741γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence