6CSW

Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VRK1A, B, C, D364Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FBY (Subject of Investigation/LOI)
Query on FBY

Download Ideal Coordinates CCD File 
J [auth B], Z [auth D](7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one
C18 H21 F2 N5 O2
IQHUYDHFNRXPGH-SNVBAGLBSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A], I [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , CA [auth D] , DA [auth D] , E [auth A] , EA [auth D] , F [auth A] , FA [auth D] , 
AA [auth D],  BA [auth D],  CA [auth D],  DA [auth D],  E [auth A],  EA [auth D],  F [auth A],  FA [auth D],  K [auth B],  L [auth B],  M [auth B],  R [auth C],  S [auth C],  T [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GA [auth D] , HA [auth D] , IA [auth D] , JA [auth D] , KA [auth D] , LA [auth D] , MA [auth D] , N [auth B] , 
GA [auth D],  HA [auth D],  IA [auth D],  JA [auth D],  KA [auth D],  LA [auth D],  MA [auth D],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  U [auth C],  V [auth C],  W [auth C],  X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A], NA [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
OA [auth D], Y [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.83α = 90
b = 96.987β = 90
c = 191.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/50724-5

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-12-16
    Changes: Other, Structure summary