3WIL | pdb_00003wil

Crystal structure of the CK2alpha/compound3 complex

PDB DOI: https://doi.org/10.2210/pdb3WIL/pdb

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

Deposited: 2013-09-18 Released: 2014-09-24
Deposition Author(s): Kinoshita, T., Nakanishi, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.281 (Depositor), 0.314 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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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: 40.83 kDa
Atom Count: 2,870
Modeled Residue Count: 331
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
LCD Query on LCD 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]	{[(2Z)-2-(3,4-dimethoxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-6-yl]oxy}acetic acid C₁₉ H₁₆ O₇ OYUZJJUVKBNAII-IUXPMGMMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.281 (Depositor), 0.314 (DCC)
R-Value Work: 0.204 (Depositor), 0.203 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.092	α = 90
b = 78.991	β = 90
c = 82.518	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.