8ABX

Crystal structure of IDO1 in complex with Apoxidole-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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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

  • DOI: https://doi.org/10.1002/anie.202209374
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1404Homo sapiensMutation(s): 0 
Gene Names: IDO1IDOINDO
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14902
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N39 (Subject of Investigation/LOI)
Query on N39

Download Ideal Coordinates CCD File 
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
N2U (Subject of Investigation/LOI)
Query on N2U

Download Ideal Coordinates CCD File 
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
PG4
Query on PG4

Download Ideal Coordinates CCD File 
B [auth A],
F [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
G [auth A],
H [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.48α = 90
b = 109.49β = 90
c = 36.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyEFRE-0200481

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-09-07
    Changes: Database references
  • Version 1.3: 2022-10-05
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description