9ZF4 | pdb_00009zf4

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83

PDB DOI: https://doi.org/10.2210/pdb9ZF4/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-12-01 Released: 2026-04-22
Deposition Author(s): Litchfield, C.M., Abiodun, W.O., 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: 2.09 Å
R-Value Free:
0.224 (Depositor), 0.226 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (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

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83

Litchfield, C.M., Abiodun, W.O., Burtch, M., Cartwright, J., Dass, R., Singleton, J.D., Doukov, T., Peterson, M.A., Moody, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 69.32 kDa
Atom Count: 4,555
Modeled Residue Count: 536
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	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C15 (Subject of Investigation/LOI) Query on A1C15 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]	methyl 2-[(8R)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazole-6-carboxylate C₁₅ H₁₀ N₄ O₂ S FWGOLGYKBZCRKS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.224 (Depositor), 0.226 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.074	α = 90
b = 113.074	β = 90
c = 145.461	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM146209
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM155011