9F5R | pdb_00009f5r

Holo IDO with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb9F5R/pdb

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

Deposited: 2024-04-30 Released: 2025-05-14
Deposition Author(s): Wicki, M., Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.239 (Depositor), 0.232 (DCC)
R-Value Work:
0.217 (Depositor), 0.207 (DCC)
R-Value Observed:
0.218 (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: 96.43 kDa
Atom Count: 6,564
Modeled Residue Count: 767
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
A1H93 (Subject of Investigation/LOI) Query on A1H93 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	(R)-[1-[2,5-bis(fluoranyl)-4-methoxy-phenyl]-1,2,3-triazol-4-yl]-(6-cyclopropylimidazo[1,5-a]pyrazin-5-yl)methanol C₁₉ H₁₆ F₂ N₆ O₂ FQZYKWGHIWGNGJ-IBGZPJMESA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]