7BU4 | pdb_00007bu4

Crystal structure of CK2a1 complexed with KY49

• PDB DOI: https://doi.org/10.2210/pdb7BU4/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-04 Released: 2021-04-07 
• Deposition Author(s): Tsuyuguchi, M., Kinoshita, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and SAR studies of protein kinase CK2 inhibitors with a purine scaffold

Nishiwaki, K., Nakamura, S., Tsuyuguchi, M., Kinoshita, T., Nakanishi, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.85 kDa 
• Atom Count: 3,037 
• Modeled Residue Count: 334 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein Kinase 2 subunit alpha	A	340	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y49 (Subject of Investigation/LOI)	B [auth A]	4-(6-aminocarbonyl-8-oxidanylidene-9-phenyl-7H-purin-2-yl)benzoic acid C19 H13 N5 O4 ZIQWXRLSVVVXBM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.27	α = 90
b = 82.82	β = 90
c = 79.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Tsuyuguchi, M., Kinoshita, T.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Advisory, Data collection, Database references, Refinement description