6K3L | pdb_00006k3l

Crystal structure of CX-4945 bound Cka1 from C. neoformans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.219 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6K3L

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of fungal pathogenicity-related casein kinase alpha subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans.

Ong, B.X.Yoo, Y.Han, M.G.Park, J.B.Choi, M.K.Choi, Y.Shin, J.S.Bahn, Y.S.Cho, H.S.

(2019) Sci Rep 9: 14398-14398

  • DOI: https://doi.org/10.1038/s41598-019-50678-z
  • Primary Citation Related Structures: 
    6K3L, 6KO6

  • PubMed Abstract: 

    CK2α is a constitutively active and highly conserved serine/threonine protein kinase that is involved in the regulation of key cellular metabolic pathways and associated with a variety of tumours and cancers. The most well-known CK2α inhibitor is the human clinical trial candidate CX-4945, which has recently shown to exhibit not only anti-cancer, but also anti-fungal properties. This prompted us to work on the CK2α orthologue, Cka1, from the pathogenic fungus Cryptococcus neoformans, which causes life-threatening systemic cryptococcosis and meningoencephalitis mainly in immunocompromised individuals. At present, treatment of cryptococcosis remains a challenge due to limited anti-cryptococcal therapeutic strategies. Hence, expanding therapeutic options for the treatment of the disease is highly clinically relevant. Herein, we report the structures of Cka1-AMPPNP-Mg 2+ (2.40 Å) and Cka1-CX-4945 (2.09 Å). Structural comparisons of Cka1-AMPPNP-Mg 2+ with other orthologues revealed the dynamic architecture of the N-lobe across species. This may explain for the difference in binding affinities and deviations in protein-inhibitor interactions between Cka1-CX-4945 and human CK2α-CX-4945. Supporting it, in vitro kinase assay demonstrated that CX-4945 inhibited human CK2α much more efficiently than Cka1. Our results provide structural insights into the design of more selective inhibitors against Cka1.


  • Organizational Affiliation
    • Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 40.03 kDa 
  • Atom Count: 2,868 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 338 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CMGC/CK2 protein kinaseA [auth B]338Cryptococcus neoformans H99Mutation(s): 0 
Gene Names: CNAG_05694
EC: 2.7.11.1
UniProt
Find proteins for J9VNH4 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VNH4 
Go to UniProtKB:  J9VNH4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VNH4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NG
(Subject of Investigation/LOI)

Query on 3NG



Download:Ideal Coordinates CCD File
B
5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C19 H12 Cl N3 O2
MUOKSQABCJCOPU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.219 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.762α = 90
b = 95.395β = 90
c = 94.518γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description