8R5Q

Structure of apo TDO with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb8R5Q/pdb

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

Deposited: 2023-11-17 Released: 2024-01-17
Deposition Author(s): Wicki, M., Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.267
R-Value Work: 0.254
R-Value Observed: 0.255

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

Discovery and binding mode of a small molecule inhibitor of the apo form of human TDO2

Lotz-Jenne, C., Lange, R., Cren, S., Bourquin, G., Goglia, L., Kimmerlin, T., Wicki, M., Mueller, M., Artico, N., Ackerknecht, S., Joesch, C., Mac Sweeney, A.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.01.09.574827

Macromolecule Content

Total Structure Weight: 173.76 kDa
Atom Count: 9,960
Modelled Residue Count: 1,263
Deposited Residue Count: 1,432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	358	Homo sapiens	Mutation(s): 0 Gene Names: TDO2 EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens) Explore P48775 Go to UniProtKB: P48775
PHAROS: P48775 GTEx: ENSG00000151790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48775
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y5N (Subject of Investigation/LOI) Query on Y5N Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	3-chloranyl-~{N}-[(1~{S})-1-(6-chloranylpyridin-3-yl)-2-phenyl-ethyl]aniline C₁₉ H₁₆ Cl₂ N₂ FPQMXEJXTNDYME-SFHVURJKSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
ZIQ Query on ZIQ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	alpha-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ ZTTWHZHBPDYSQB-LBPRGKRZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]