7M63 | pdb_00007m63

Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with IACS-70099


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of IACS-9779 and IACS-70465 as Potent Inhibitors Targeting Indoleamine 2,3-Dioxygenase 1 (IDO1) Apoenzyme.

Hamilton, M.M.Mseeh, F.McAfoos, T.J.Leonard, P.G.Reyna, N.J.Harris, A.L.Xu, A.Han, M.Soth, M.J.Czako, B.Theroff, J.P.Mandal, P.K.Burke, J.P.Virgin-Downey, B.Petrocchi, A.Pfaffinger, D.Rogers, N.E.Parker, C.A.Yu, S.S.Jiang, Y.Krapp, S.Lammens, A.Trevitt, G.Tremblay, M.R.Mikule, K.Wilcoxen, K.Cross, J.B.Jones, P.Marszalek, J.R.Lewis, R.T.

(2021) J Med Chem 64: 11302-11329

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00679
  • Primary Citation Related Structures: 
    7B1O, 7M63, 7M7D

  • PubMed Abstract: 

    Indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme that mediates the rate-limiting step in the metabolism of l-tryptophan to kynurenine, has been widely explored as a potential immunotherapeutic target in oncology. We developed a class of inhibitors with a conformationally constrained bicyclo[3.1.0]hexane core. These potently inhibited IDO1 in a cellular context by binding to the apoenzyme, as elucidated by biochemical characterization and X-ray crystallography. A SKOV3 tumor model was instrumental in differentiating compounds, leading to the identification of IACS-9779 ( 62 ) and IACS-70465 ( 71 ). IACS-70465 has excellent cellular potency, a robust pharmacodynamic response, and in a human whole blood assay was more potent than linrodostat (BMS-986205). IACS-9779 with a predicted human efficacious once daily dose below 1 mg/kg to sustain >90% inhibition of IDO1 displayed an acceptable safety margin in rodent toxicology and dog cardiovascular studies to support advancement into preclinical safety evaluation for human development.


  • Organizational Affiliation
    • IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States.

Macromolecule Content 

  • Total Structure Weight: 93.42 kDa 
  • Atom Count: 5,924 
  • Modeled Residue Count: 739 
  • Deposited Residue Count: 822 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1
A, B
411Homo 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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YRP
(Subject of Investigation/LOI)

Query on YRP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(2R)-N-(4-chlorophenyl)-2-[(1R,3S,5S,6r)-3-(5,6-difluoro-1H-benzimidazol-1-yl)bicyclo[3.1.0]hexan-6-yl]propanamide
C22 H20 Cl F2 N3 O
FVIXADGZFNVGRM-IDJJVQAESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.91α = 90
b = 92.07β = 90
c = 128.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary