8V42 | pdb_00008v42

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.203 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1 delta / epsilon.

de Souza Gama, F.H.Dutra, L.A.Hawgood, M.Dos Reis, C.V.Serafim, R.A.M.Ferreira Jr., M.A.Teodoro, B.V.M.Takarada, J.E.Santiago, A.S.Balourdas, D.I.Nilsson, A.S.Urien, B.Almeida, V.M.Gileadi, C.Ramos, P.Z.Salmazo, A.Vasconcelos, S.N.S.Cunha, M.R.Mueller, S.Knapp, S.Massirer, K.B.Elkins, J.M.Gileadi, O.Mascarello, A.Lemmens, B.B.L.G.Guimaraes, C.R.W.Azevedo, H.Counago, R.M.

(2024) J Med Chem 67: 8609-8629

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02250
  • Primary Citation Related Structures: 
    8V42

  • PubMed Abstract: 

    Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.


  • Organizational Affiliation
    • Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil.

Macromolecule Content 

  • Total Structure Weight: 165.9 kDa 
  • Atom Count: 9,908 
  • Modeled Residue Count: 1,229 
  • 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
YD9

Query on YD9



Download:Ideal Coordinates CCD File
F [auth B],
K [auth D]
(7S)-2-(3,5-difluoro-4-hydroxyanilino)-7-methyl-5-[(1,2-oxazol-5-yl)methyl]-8-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
C20 H16 F2 N6 O3
DFEBWFCZSQPYKA-NSHDSACASA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth C],
H [auth C],
I [auth D],
J [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.552α = 90
b = 96.615β = 90
c = 190.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release