9S1V | pdb_00009s1v

Crystal structure of human IDO1 in complex with iDeg-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Design, Synthesis, and Structural Evolution of Pseudo-Natural Product IDO1 Inhibitors and Degraders.

Cheng, X.F.Lucas, B.Lampe, P.Ugel, S.Chen, S.Unger, A.Bischoff, M.Adariani, S.R.Naredla, K.R.Kumar, K.Schmidt, A.Strohmann, C.Janning, P.Gasper, R.Lucas, M.Gersch, M.Sievers, S.Bronte, V.Ziegler, S.Waldmann, H.

(2025) Angew Chem Int Ed Engl : e18753-e18753

  • DOI: https://doi.org/10.1002/anie.202518753
  • Primary Citation of Related Structures:  
    9S1U, 9S1V, 9S1W, 9S1X

  • PubMed Abstract: 

    Terpenoid alkaloids are derived from the fusion of structurally diverse terpenoid- and alkaloid moieties. The biologically relevant chemical space defined by this unique natural product (NP) class may be explored beyond the limitations of biosynthetic pathways by means of the pseudo natural product (PNP) principle, i.e., by combination of NP fragments in different arrangements. We describe the design, synthesis and structural evolution of a monoterpene-pyrrolidine PNP collection obtained by functionalization and combination of bicyclic monoterpenes with pyrrolidine alkaloid-derived fragments. Diverse fusion strategies led to the discovery of (-)-myrtenal-pyrrolidine PNPs that are indoleamine-2,3-dioxygenase 1 (IDO1) inhibitors and degraders, termed iDegs. Structural fine-tuning modulated both degradation and inhibition potencies. Co-crystallization revealed that iDegs induce unprecedented changes in the C-terminus of IDO1 which promote degradation. iDegs inhibited tumor growth in SKOV-3 tumor-bearing mice and led to prolonged survival, which promises to inspire novel medicinal chemistry programs aimed at IDO1 in different diseases.


  • Organizational Affiliation
    • Abteilung Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JLD (Subject of Investigation/LOI)
Query on A1JLD

Download Ideal Coordinates CCD File 
E [auth A][(1~{R},2~{S},6~{S},8~{R})-4-(4-~{tert}-butyl-2-methyl-phenyl)sulfonyl-9,9-dimethyl-4-azatricyclo[6.1.1.0^{2,6}]decan-2-yl]methyl ~{N}-(4-ethynylphenyl)carbamate
C32 H40 N2 O4 S
SVVLXZSOWBLJBW-YUGNUMPCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.78α = 90
b = 109.91β = 90
c = 36.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release