6NCG | pdb_00006ncg

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.297 (Depositor), 0.299 (DCC)
R-Value Work:
0.221 (Depositor), 0.230 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86Y07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KJD Query on KJD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.297 (Depositor), 0.299 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

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

Revision History (Full details and data files)

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