Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 166712.95 
• Atom Count: 9303 
• Residue Count: 1452 
• Unique protein chains: 1

5UKF

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

• DOI: 10.2210/pdb5UKF/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 11 


• Deposited: 2017-01-22 Released: 2017-03-29 
• Deposition Author(s): Counago, R.M., Wells, C., Zuercher, W., Willson, T.M., Bountra, C., Edwards, A.M., Arruda, P., Gileadi, O., Structural Genomics Consortium (SGC)
• Funding Organization(s): FAPESP 

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Experimental Data Snapshot

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

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

• PubMed: 28790404 
• Primary Citation of Related Structures:  
  3OP5, 5UVF, 5UU1

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase VRK1	A, B, C, D	363	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
8E1	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
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
PEG	D	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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 = 92.138	α = 90.00
b = 96.051	β = 90.00
c = 192.741	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-22 
• Released Date: 2017-03-29 
• Deposition Author(s): Counago, R.M., Wells, C., Zuercher, W., Willson, T.M., Bountra, C., Edwards, A.M., Arruda, P., Gileadi, O., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
FAPESP	Brazil	13/50724-5

Revision History 

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