3WIK | pdb_00003wik

Crystal structure of the CK2alpha/compound10 complex

PDB DOI: https://doi.org/10.2210/pdb3WIK/pdb

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

Deposited: 2013-09-18 Released: 2014-11-05
Deposition Author(s): Kinoshita, T., Nakaniwa, T., Sekiguchi, Y., Nakanishi, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.211 (Depositor), 0.201 (DCC)
R-Value Work:
0.163 (Depositor)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3WIK

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of protein kinase CK2 inhibitors using solvent dipole ordering virtual screening

Nakanishi, I., Murata, K., Nagata, N., Kurono, M., Kinoshita, T., Yasue, M., Miyazaki, T., Hirasawa, A., Tsujimoto, G., Kitaura, K.

To be published.

Macromolecule Content

Total Structure Weight: 40.74 kDa
Atom Count: 2,991
Modeled Residue Count: 334
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	340	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68400
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LCT Query on LCT 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-(4-nitrophenyl)-1,3,4-thiadiazol-2-yl]acetamide C₁₀ H₈ N₄ O₃ S KTJUGKNFZGGFIC-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LCT	BindingDB: 3WIK	IC50: min: 2.68e+4, max: 3.22e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211 (Depositor), 0.201 (DCC)
R-Value Work: 0.163 (Depositor)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.382	α = 90
b = 79.451	β = 90
c = 82.888	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.