6DD4

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor

dos Reis, C.V.Santiago, A.S.de Souza, G.P.Counago, R.M.Azevedo, H.Guimaraes, C.Mascarello, A.Gama, F.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
G6J (Subject of Investigation/LOI)
Query on G6J

Download Ideal Coordinates CCD File 
M [auth B], Y [auth D](7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-dipropyl-7,8-dihydropteridin-6(5H)-one
C19 H23 F2 N5 O2
OQSCAKQGDHBTSX-LLVKDONJSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D], N [auth B], O [auth B], P [auth B], T [auth C], Z [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth B], X [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth D], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], W [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], U [auth C], V [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.596α = 90
b = 96.168β = 90
c = 191.871γ = 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: 2018-05-23
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-12-16
    Changes: Database references, Other, Structure summary