6VZH | pdb_00006vzh

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.251 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VZH

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

dos Reis, C.V., Dutra, L.A., Gama, F., Ferreira, M., Mascarello, A., Azevedo, H., Guimaraes, C.R.W., Massirer, K.B., Arruda, P., Edwards, A.M., Counago, R.M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 166.2 kDa 
  • Atom Count: 9,695 
  • Modeled Residue Count: 1,244 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VRK1
A, B, C, D
364Homo 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
GTEx:  ENSG00000100749 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99986
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RYA
(Subject of Investigation/LOI)

Query on RYA


Download:Ideal Coordinates CCD File
J [auth B],
P [auth D]		(7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one
C17 H15 F2 N5 O2
DYKLQWQETZOVEI-SECBINFHSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO


Download:Ideal Coordinates CCD File
O [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RYA BindingDB:  6VZH Ki: 135 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.251 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.158α = 90
b = 95.641β = 90
c = 192.593γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/50724-5
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil465651/2014-3
Sao Paulo Research Foundation (FAPESP)Brazil2014/50897-0

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description