6BP0

Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor

Counago, R.M.dos Reis, C.V.de Souza, G.P.Azevedo, A.Guimaraes, C.Mascarello, A.Gama, F.Ferreira, M.Massirer, K.B.Arruda, P.Edwards, A.M.Elkins, J.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
SO4
Query on SO4

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

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Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
E1D
Query on E1D

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Download CCD File 
B, D
(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one
C15 H15 F2 N5 O2
GSJOYFAUMSHIJL-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.222α = 90.00
b = 95.118β = 90.00
c = 193.553γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references, Structure summary
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Type: Author supporting evidence