8Q9S

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR SGC-CK2-1

PDB DOI: https://doi.org/10.2210/pdb8Q9S/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-08-21 Released: 2023-12-06
Deposition Author(s): Werner, C., Lindenblatt, D., Niefind, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.169
R-Value Work: 0.135
R-Value Observed: 0.137

Starting Model: experimental
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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

DOI: https://doi.org/10.3390/kinasesphosphatases1040018

Macromolecule Content

Total Structure Weight: 43.38 kDa
Atom Count: 3,111
Modelled Residue Count: 327
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha'	A	364	Homo sapiens	Mutation(s): 1 Gene Names: CSNK2A2, CK2A2 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QBE (Subject of Investigation/LOI) Query on QBE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{N}-[5-[[3-cyano-7-(cyclopropylamino)-3~{H}-pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide C₂₀ H₂₁ N₇ O YKDZIFFKQUNVHH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QBE	BindingDB: 8Q9S	IC50: 19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.169
R-Value Work: 0.135
R-Value Observed: 0.137
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.217	α = 66.83
b = 47.682	β = 89.43
c = 50.562	γ = 88.93

Software Package:

Software Name	Purpose
autoPROC	data processing
PHENIX	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Lindenblatt, D.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	NI 643/11-1
German Research Foundation (DFG)	Germany	NI 643/4-2

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.