9FOZ | pdb_00009foz

Cocrystal structure of IDO with a bound inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.239 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cellular Potency Optimization of Novel Heme-Binding Imidazo[5,1- b ]thiazoles, Imidazo[1,5- a ]pyridines and Pyrazines as Potent IDO1 Inhibitors Devoid of Cytochrome P450 Inhibition.

Cren, S.Lotz-Jenne, C.Kimmerlin, T.Pothier, J.Risch, P.Mac Sweeney, A.Joesch, C.Pouzol, L.Chavanton-Arpel, A.Boss, C.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01067
  • Primary Citation of Related Structures:  
    9FON, 9FOZ

  • PubMed Abstract: 

    Indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase 2 (TDO2) are key enzymes in the kynurenine pathway of the catabolism of the essential amino acid tryptophan. Both enzymes actively contribute to the immunosuppressive microenvironment in many types of cancer. Selective or dual inhibition of these enzymes could, therefore, be beneficial in combination with other immunotherapies such as immune-checkpoint therapy. In a fragment-based approach, we optimized fragment 3 into a series of potent imidazo[5,1- b ]thiazole, imidazo[1,5- a ]pyridine and pyrazine IDO1 inhibitors. The introduction of the triazole side chain resulted in a reduced enzyme-to-cell potency shift for IDO1 inhibition, albeit at the expense of TDO2 potency, and allowed the discovery of potent and cellular active IDO1 inhibitors. Moreover, despite the propensity of the imidazole motif to inhibit cytochrome P450 enzymes (CYP), we were able to discover potent IDO1 inhibitors devoid of CYP inhibition. Imidazo[1,5- a ]pyrazine ( R )-100 has an overall suitable profile, which warrants further investigation.


  • Organizational Affiliation
    • Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1
A, B
418Homo 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
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1H93 (Subject of Investigation/LOI)
Query on A1H93

Download Ideal Coordinates CCD File 
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
DMS
Query on DMS

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.239 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.922α = 90
b = 92.293β = 90
c = 131.637γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Structure summary
  • Version 1.2: 2025-10-08
    Changes: Database references, Structure summary