8BI6 | pdb_00008bi6

Crystal structure of human Choline Kinase A in complex with UNC0638

PDB DOI: https://doi.org/10.2210/pdb8BI6/pdb

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

Deposited: 2022-11-01 Released: 2023-11-15
Deposition Author(s): Diaz-Saez, L., Ward, J., Kennedy, E., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K., Structural Genomics Consortium (SGC)
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.221 (Depositor), 0.225 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human Choline Kinase A in complex with UNC0638

Diaz-Saez, L., Kennedy, E., von Delft, F., Knapp, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K.

To be published.

Macromolecule Content

Total Structure Weight: 107.25 kDa
Atom Count: 6,556
Modeled Residue Count: 709
Deposited Residue Count: 914
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase alpha	A, B	457	Homo sapiens	Mutation(s): 0 Gene Names: CHKA, CHK, CKI EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens) Explore P35790 Go to UniProtKB: P35790
PHAROS: P35790 GTEx: ENSG00000110721
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35790
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIQ (Subject of Investigation/LOI) Query on CIQ Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain D [auth A] MOL2 format, chain S [auth B] MOL2 format, chain D [auth A] mmCIF format, chain S [auth B] mmCIF format, chain D [auth A]	D [auth A], S [auth B]	2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine C₃₀ H₄₇ N₅ O₂ QOECJCJVIMVJGX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain S [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain O [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain O [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain O [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B], BA [auth B], O [auth A], Z [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain O [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain O [auth A] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions 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 J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density 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 J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain N [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain N [auth A]	N [auth A], Y [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Y [auth B] Interactions & Density Focus chain N [auth A] Focus chain Y [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain CA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain CA [auth B]	CA [auth B], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain CA [auth B] Focus chain P [auth A] Focus chain Q [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain C [auth A]	C [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]