9KXV | pdb_00009kxv

Structure of human B0AT1-ACE2 complex with compound3

PDB DOI: https://doi.org/10.2210/pdb9KXV/pdb
EM Map EMD-62629: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-12-07 Released: 2025-12-10
Deposition Author(s): Imazu, T., Miyaguchi, I., Hiraizumi, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KXV

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

Literature

Structure-guided development of a potent human B0AT1 inhibitor effective in a mouse model of phenylketonuria

Imazu, T., Akashi, T., Hiraizumi, M., Inui, Y., Sasaki, W., Takahashi, T., Todoroki, H., Kumanomidou, T., Hisano, H., Asada, H., Kusakizako, T., Nishizawa, T., Iwata, S., Nureki, O., Miyaguchi, I.

To be published.

Macromolecule Content

Total Structure Weight: 166.58 kDa
Atom Count: 4,887
Modeled Residue Count: 609
Deposited Residue Count: 1,460
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent neutral amino acid transporter B(0)AT1	A	654	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A19, B0AT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q695T7 (Homo sapiens) Explore Q695T7 Go to UniProtKB: Q695T7
PHAROS: Q695T7 GTEx: ENSG00000174358
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q695T7
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q695T7-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	B	806	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L6W (Subject of Investigation/LOI) Query on A1L6W 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]	(~{E})-~{N}-[2-oxidanylidene-2-(3-oxidanylidenepiperazin-1-yl)ethyl]-3-[4-(trifluoromethyl)phenyl]prop-2-enamide C₁₆ H₁₆ F₃ N₃ O₃ SQCPJGHMDVTIRR-ZZXKWVIFSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0267

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-10
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.