7AY9 | pdb_00007ay9

Crystal structure of CK2 bound by compound 7

PDB DOI: https://doi.org/10.2210/pdb7AY9/pdb

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

Deposited: 2020-11-11 Released: 2021-11-24
Deposition Author(s): Ferguson, A., Collie, G.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7AY9

Ligand Structure Quality Assessment

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

Literature

Metadynamics simulations of CK2 compound unbinding to understand slow dissociation kinetics.

Date, M.

To be published.

Macromolecule Content

Total Structure Weight: 85.45 kDa
Atom Count: 6,190
Modeled Residue Count: 662
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	342	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S92 (Subject of Investigation/LOI) Query on S92 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain I [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain I [auth A]	I [auth A], Z [auth B]	7-(cyclopropylamino)-5-(5-(6-oxo-1,6-dihydropyridin-3-yl)-1-(2-(piperidin-1-yl)ethyl)-1H-1,2,3-triazol-4-yl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile C₂₄ H₂₆ N₁₀ O DSBYVYTVSKXJPZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain Z [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] 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 U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain C [auth A] 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 U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain GA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.207 (Depositor), 0.207 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.449	α = 90
b = 127.449	β = 90
c = 124.839	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-11-24
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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