9DKP | pdb_00009dkp

The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53

PDB DOI: https://doi.org/10.2210/pdb9DKP/pdb

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

Deposited: 2024-09-09 Released: 2025-09-17
Deposition Author(s): Abiodun, W.O., Tsubaki, E., Dass, R., Singleton, J.D., Samarawickrama, P., Doukov, T., Peterson, M.A., Moody, J.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Facile Bacterial Production of Human Vacuolar Protein Sorting 34 Enables Structural Characterization of Novel Inhibitors

Abiodun, W.O., Dass, R., Tsubaki, E., Singleton, J.D., Fullmer, A., Cartwright, J., Litchfield, C., Samarawickrama, P., Doukov, T., Peterson, M.A., Moody, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 69.26 kDa
Atom Count: 4,346
Modeled Residue Count: 530
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	A [auth B]	594	Homo sapiens	Mutation(s): 0 Gene Names: PIK3C3, VPS34 EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens) Explore Q8NEB9 Go to UniProtKB: Q8NEB9
PHAROS: Q8NEB9 GTEx: ENSG00000078142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NEB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A6F (Subject of Investigation/LOI) Query on A1A6F Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	(8R)-3-(1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine C₁₃ H₈ N₄ S SAZAMNXEWSKXHU-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
ETX Query on ETX Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ETZ Query on ETZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	D [auth B], E [auth B]	diethyl ether C₄ H₁₀ O RTZKZFJDLAIYFH-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]