6BU6

Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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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 bis-difluorophenol-aminopyridine inhibitor

Counago, R.M.dos Reis, C.V.de Souza, G.P.Santiago, A.S.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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E8V (Subject of Investigation/LOI)
Query on E8V

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], P [auth D]4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol)
C17 H10 F4 N2 O2
FFWVPGLOKRROCI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], S [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.215α = 90
b = 96.572β = 90
c = 193.056γ = 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: 2017-12-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence