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), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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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

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 D [auth A] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain S [auth B]	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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain O [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Z [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 E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [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 N [auth A] SDF format, chain Y [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B]	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 CA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	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 C [auth A] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain R [auth B]	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]