9EW0 | pdb_00009ew0

Holo IDO with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb9EW0/pdb

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

Deposited: 2024-04-03 Released: 2025-04-02
Deposition Author(s): Wicki, M., Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.278 (Depositor)
R-Value Work:
0.249 (Depositor)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 95.86 kDa
Atom Count: 6,219
Modeled Residue Count: 749
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B	418	Homo sapiens	Mutation(s): 0 Gene Names: IDO1, IDO, INDO EC: 1.13.11.52
UniProt & NIH Common Fund Data Resources
Find proteins for P14902 (Homo sapiens) Explore P14902 Go to UniProtKB: P14902
PHAROS: P14902 GTEx: ENSG00000131203
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14902
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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
A1H6U (Subject of Investigation/LOI) Query on A1H6U Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	(~{S})-cyclohexyl(imidazo[1,5-a]pyridin-5-yl)methanol C₁₄ H₁₈ N₂ O MHPBLJWAAANDQV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.278 (Depositor)
R-Value Work: 0.249 (Depositor)
R-Value Observed: 0.251 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.05	α = 90
b = 92.891	β = 90
c = 129.357	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Mac Sweeney, A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
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.