9D2P | pdb_00009d2p

PANK3 complex structure with compound PZ-4127

PDB DOI: https://doi.org/10.2210/pdb9D2P/pdb

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

Deposited: 2024-08-09 Released: 2025-08-13
Deposition Author(s): Yun, M., Lee, R.E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.220 (Depositor), 0.223 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (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

2-(4-aminophenyl)acetamide derivatives as Pantothenate Kinase Inhibitors.

Yun, M., Lee, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 43.13 kDa
Atom Count: 2,904
Modeled Residue Count: 352
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate kinase 3	A	380	Homo sapiens	Mutation(s): 0 Gene Names: PANK3 EC: 2.7.1.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H999 (Homo sapiens) Explore Q9H999 Go to UniProtKB: Q9H999
PHAROS: Q9H999 GTEx: ENSG00000120137
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H999
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MZI (Subject of Investigation/LOI) Query on MZI 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]	2-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}anilino)-2-oxoethyl acetate C₂₀ H₂₂ Cl N₅ O₄ MASGWEOQCQKQCO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACY Query on ACY 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]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]