6NCG

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6NCG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-11 Released: 2019-01-16 
• Deposition Author(s): dos Reis, C.V., Chiodi, C.G., de Souza, G.P., Guimaraes, C., Mascarello, A., Gama, F., Ferreira, M., Counago, R.M., Massirer, K.B., Elkins, J.M., Arruda, P., Edwards, A.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor

dos Reis, C.V., Chiodi, C.G., de Souza, G.P., Azevedo, H., Guimaraes, C., Mascarello, A., Gama, F., Ferreira, M., Counago, R.M., Massirer, K.B., Arruda, P., Elkins, J.M., Edwards, A.M., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.43 kDa 
• Atom Count: 4,564 
• Modelled Residue Count: 595 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase VRK2	A, B	324	Homo sapiens	Mutation(s): 0  Gene Names: VRK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y07 (Homo sapiens) Explore Q86Y07  Go to UniProtKB:  Q86Y07
PHAROS:  Q86Y07 GTEx:  ENSG00000028116

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KJD	C [auth A], E [auth B]	4-[6-amino-5-(3,5-difluoro-4-hydroxyphenyl)pyridin-3-yl]benzene-1-sulfonamide C17 H13 F2 N3 O3 S MTBXQYCZMOAADV-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
KJD	BindingDB:  6NCG	Kd: 401 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.528	α = 90
b = 67.625	β = 90
c = 171.346	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): dos Reis, C.V., Chiodi, C.G., de Souza, G.P., Guimaraes, C., Mascarello, A., Gama, F., Ferreira, M., Counago, R.M., Massirer, K.B., Elkins, J.M., Arruda, P., Edwards, A.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description