9ETV | pdb_00009etv

Holo IDO with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb9ETV/pdb

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

Deposited: 2024-03-27 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: 2.40 Å
R-Value Free:
0.290 (Depositor), 0.264 (DCC)
R-Value Work:
0.260 (Depositor), 0.246 (DCC)
R-Value Observed:
0.261 (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

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: 44.05 kDa
Atom Count: 2,889
Modeled Residue Count: 341
Deposited Residue Count: 365
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	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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
A1H61 (Subject of Investigation/LOI) Query on A1H61 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]	6-methylimidazo[1,5-a]pyridine C₈ H₈ N₂ LOHYEHLOEQRDHI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.290 (Depositor), 0.264 (DCC)
R-Value Work: 0.260 (Depositor), 0.246 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.382	α = 90
b = 113.382	β = 90
c = 213.926	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-05

Deposition Author(s):

Mac Sweeney, A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-03-05
Type: Initial release

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.