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: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.1 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VRK1A, B, C, D364Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCS (Subject of Investigation/LOI)
Query on FCS

Download Ideal Coordinates CCD File 
O [auth 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
F87 (Subject of Investigation/LOI)
Query on F87

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], U [auth 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

Download Ideal Coordinates CCD File 
F [auth A], P [auth C], V [auth D], W [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth D] , G [auth A] , H [auth A] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , Q [auth C] , 
AA [auth D], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], X [auth D], Y [auth D], Z [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.47α = 90
b = 96.821β = 90
c = 192.831γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2018-04-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence