5CQW

Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry

PDB DOI: https://doi.org/10.2210/pdb5CQW/pdb
Entry: 5CQW supersedes: 4BXA

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-22 Released: 2015-09-09
Deposition Author(s): Niefind, K., Schnitzler, A., Swider, R., Maslyk, M., Ramos, A.
Funding Organization(s): German Research Foundation, Spanisch Ministry of Science and Innovation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.229
R-Value Work: 0.182
R-Value Observed: 0.185

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis, Biological Activity and Structural Study of New Benzotriazole-Based Protein Kinase CK2 Inhibitors

Swider, R., Maslyk, M., Zapico, J.M., Coderch, C., Panchuk, R., Skorokhyd, N., Schnitzler, A., Niefind, K., de Pascual-Teresa, B., Ramos, A.

(2015) RSC Adv 5: 72482-72494

DOI: https://doi.org/10.1039/C5RA12114K

Macromolecule Content

Total Structure Weight: 82.83 kDa
Atom Count: 5,893
Modelled Residue Count: 662
Deposited Residue Count: 670
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, B	335	Homo sapiens	Mutation(s): 0 Gene Names: CSNK2A1, CK2A1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68400
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JRJ Query on JRJ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	C [auth A], M [auth B]	4-[4-[2-[4,5,6,7-tetrakis(bromanyl)benzotriazol-2-yl]ethyl]-1,2,3-triazol-1-yl]butan-1-amine C₁₄ H₁₅ Br₄ N₇ KAIWWTMLTRXFON-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A]	K [auth A], L [auth A], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B]	J [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.229
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.092	α = 90
b = 127.092	β = 90
c = 126.836	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

This entry supersedes: 4BXA

Funding Organization	Location	Grant Number
German Research Foundation	Germany	NI 643/4-1
Spanisch Ministry of Science and Innovation	Spain	CTQ2011-24741

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description