8ABX | pdb_00008abx

Crystal structure of IDO1 in complex with Apoxidole-1

PDB DOI: https://doi.org/10.2210/pdb8ABX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-05 Released: 2022-08-24
Deposition Author(s): Dotsch, L., Ziegler, S., Waldmann, H., Gasper, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype.

Davies, C., Dotsch, L., Ciulla, M.G., Hennes, E., Yoshida, K., Gasper, R., Scheel, R., Sievers, S., Strohmann, C., Kumar, K., Ziegler, S., Waldmann, H.

(2022) Angew Chem Int Ed Engl 61: e202209374-e202209374

PubMed: 35959923 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202209374
Primary Citation Related Structures:
8ABX

PubMed Abstract:
Natural product (NP)-inspired design principles provide invaluable guidance for bioactive compound discovery. Pseudo-natural products (PNPs) are de novo combinations of NP fragments to target biologically relevant chemical space not covered by NPs. We describe the design and synthesis of apoxidoles, a novel pseudo-NP class, whereby indole- and tetrahydropyridine fragments are linked in monopodal connectivity not found in nature. Apoxidoles are efficiently accessible by an enantioselective [4+2] annulation reaction. Biological evaluation revealed that apoxidoles define a new potent type IV inhibitor chemotype of indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme considered a target for the treatment of neurodegeneration, autoimmunity and cancer. Apoxidoles target apo-IDO1, prevent heme binding and induce unique amino acid positioning as revealed by crystal structure analysis. Novel type IV apo-IDO1 inhibitors are in high demand, and apoxidoles may provide new opportunities for chemical biology and medicinal chemistry research.

Organizational Affiliation

Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 47.55 kDa
Atom Count: 3,357
Modeled Residue Count: 369
Deposited Residue Count: 404
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	404	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N39 (Subject of Investigation/LOI) Query on N39 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	O1-tert-butyl O2-ethyl O5-methyl (E,5R)-5-(1-methylindol-2-yl)-5-[(4-methylphenyl)sulfonylamino]pent-2-ene-1,2,5-tricarboxylate C₃₁ H₃₆ N₂ O₈ S FUSYRUNCXNWFDD-SUYBVONHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
N2U (Subject of Investigation/LOI) Query on N2U Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	O2-tert-butyl O3-ethyl O6-methyl (2S,6R)-6-(1-methylindol-2-yl)-2,5-dihydro-1H-pyridine-2,3,6-tricarboxylate C₂₄ H₃₀ N₂ O₆ KITXNGADRUMEPM-YADARESESA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain B [auth A]	B [auth A], F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain F [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], G [auth A], H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A]