8QBU

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR CX-4945 AND THE ALPHA-D-POCKET LIGAND 3,4-DICHLORO PHENETHYLAMINE (DPA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool

Werner, C.Lindenblatt, D.Viht, K.Uri, A.Niefind, K.

(2023) Kinases Phosphatases 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha'364Homo sapiensMutation(s): 1 
Gene Names: CSNK2A2CK2A2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens)
Explore P19784 
Go to UniProtKB:  P19784
PHAROS:  P19784
GTEx:  ENSG00000070770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19784
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NG (Subject of Investigation/LOI)
Query on 3NG

Download Ideal Coordinates CCD File 
F [auth A]5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C19 H12 Cl N3 O2
MUOKSQABCJCOPU-UHFFFAOYSA-N
42J (Subject of Investigation/LOI)
Query on 42J

Download Ideal Coordinates CCD File 
E [auth A]2-(3,4-dichlorophenyl)ethanamine
C8 H9 Cl2 N
MQPUAVYKVIHUJP-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
G [auth A]
H [auth A]
B [auth A],
C [auth A],
D [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3NG BindingDB:  8QBU Ki: 0.22 (nM) from 1 assay(s)
IC50: min: 0.3, max: 552 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.173α = 66.05
b = 47.715β = 89.72
c = 50.586γ = 88.97
Software Package:
Software NamePurpose
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyNI 643/11-1
German Research Foundation (DFG)GermanyNI 643/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release