6CNX

Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) bound to a N-propynyl-N-isopentil-dihydropteridine inhibitor

Counago, R.M.dos Reis, C.V.de Souza, G.P.Gama, F.Azevedo, H.Guimaraes, C.Mascarello, A.Ferreira, M.Massirer, K.B.Arruda, P.Edwards, A.M.Elkins, J.M.Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase VRK1
A, B, C, D
364Homo sapiensMutation(s): 11 
Gene Names: VRK1
EC: 2.7.11.1
Find proteins for Q99986 (Homo sapiens)
Go to Gene View: VRK1
Go to UniProtKB:  Q99986
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F87
Query on F87

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Download CCD File 
A, B, D
(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
C21 H23 F2 N5 O2
IHZPRIAIJQSUAF-CYBMUJFWSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FCS
Query on FCS

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Download CCD File 
C
(7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
C21 H23 F2 N5 O2
IHZPRIAIJQSUAF-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.470α = 90.00
b = 96.821β = 90.00
c = 192.831γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil13/50724-5

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release