9TTA | pdb_00009tta

Crystal Structure of S12 bound to Ck2a

PDB DOI: https://doi.org/10.2210/pdb9TTA/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2026-01-06 Released: 2026-05-06
Deposition Author(s): Brear, P., Day-Riley, S., Krajcovicov, S., Raj Sokha, A., Venne, J., Hyvonen, M., Whitehurst, B., Spring, D.R.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.284 (Depositor), 0.281 (DCC)
R-Value Work:
0.229 (Depositor), 0.233 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9TTA

Ligand Structure Quality Assessment

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

Literature

Towards the Targeted Protein Degradation of CK2: Design and Synthesis of CAM4066-Based PROTACs

Day-Riley, S., Krajcovicov, S., Brear, P., Raj Sokha, A., Venne, J., Hyvonen, M., Whitehurst, B., Spring, D.R.

To be published.

Macromolecule Content

Total Structure Weight: 39.74 kDa
Atom Count: 2,917
Modeled Residue Count: 327
Deposited Residue Count: 328
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	328	Homo sapiens	Mutation(s): 4 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JXM (Subject of Investigation/LOI) Query on A1JXM 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]	3-[2-[4-[(3-chloranyl-4-phenyl-phenyl)methylamino]butyl-[2-oxidanylidene-2-[2-(2-prop-2-ynoxyethoxy)ethylamino]ethyl]amino]ethanoylamino]benzoic acid C₃₅ H₄₁ Cl N₄ O₆ LUFHJVJRLWMKRW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.284 (Depositor), 0.281 (DCC)
R-Value Work: 0.229 (Depositor), 0.233 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.626	α = 90
b = 46.103	β = 111.8
c = 62.648	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Krajcovicov, S.

Funding Organization	Location	Grant Number
Other private	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release
Version 1.1: 2026-05-13
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.