5UKF

Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.

Counago, R.M.Allerston, C.K.Savitsky, P.Azevedo, H.Godoi, P.H.Wells, C.I.Mascarello, A.de Souza Gama, F.H.Massirer, K.B.Zuercher, W.J.Guimaraes, C.R.W.Gileadi, O.

(2017) Sci Rep 7: 7501-7501


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase VRK1
A, B, C, D
363Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8E1
Query on 8E1

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Download CCD File 
A, B, C, D
4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide
C16 H12 N4 O3 S2
LTYGAJVXAFJKSY-XFFZJAGNSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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
PEG
Query on PEG

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Download CCD File 
D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.138α = 90.00
b = 96.051β = 90.00
c = 192.741γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil13/50724-5

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references