9ESD | pdb_00009esd

Holo TDO with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb9ESD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-26 Released: 2025-03-05
Deposition Author(s): Wicki, M., Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.255 (Depositor), 0.249 (DCC)
R-Value Work:
0.233 (Depositor), 0.223 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SAR and cellular potency optimization of novel heme-binding IDO1 inhibitors

Cren, S., Lotz, C., Mac Sweeney, A., Lange, R., Kimmerlin, T.

To be published.

Macromolecule Content

Total Structure Weight: 176.81 kDa
Atom Count: 11,368
Modelled Residue Count: 1,329
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	365	Drosophila melanogaster	Mutation(s): 0 Gene Names: v, CG5163 EC: 1.13.11.11
UniProt
Find proteins for P20351 (Drosophila melanogaster) Explore P20351 Go to UniProtKB: P20351
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20351
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		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]
5PK (Subject of Investigation/LOI) Query on 5PK 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]	(1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol C₁₈ H₂₂ N₂ O YTRRAUACYORZLX-FUHWJXTLSA-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]