8FUR

Crystal structure of human IDO1 with compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Synthesis and biological evaluation of biaryl alkyl ethers as inhibitors of IDO1.

Markwalder, J.A.Balog, A.J.Williams, D.K.Nara, S.J.Reddy, R.Roy, S.Kanyaboina, Y.Li, X.Johnston, K.Fan, Y.Lewis, H.Marsilio, F.Yan, C.Critton, D.Newitt, J.A.Traeger, S.C.Wu, D.R.Jure-Kunkel, M.N.Jayaraman, L.Lin, T.A.Sinz, M.W.Hunt, J.T.Seitz, S.P.

(2023) Bioorg Med Chem Lett 88: 129280-129280

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129280
  • Primary Citation of Related Structures:  
    8FUR

  • PubMed Abstract: 

    Starting from the dialkylaniline indoleamine 2,3-dioxygenase 1 (IDO1) inhibitor lead 3 (IDO1 HeLa IC 50  = 7.0 nM), an iterative process of synthesis and screening led to cyclized analog 21 (IDO1 HeLa IC 50  = 3.6 nM) which maintained the high potency of 3 while addressing issues of lipophilicity, cytochrome P450 (CYP) inhibition, hERG (human potassium ion channel Kv11.1) inhibition, Pregnane X Receptor (PXR) transactivation, and oxidative metabolic stability. An x-ray crystal structure of a biaryl alkyl ether 11 bound to IDO1 was obtained. Consistent with our earlier results, compound 11 was shown to bind to the apo form of the enzyme.


  • Organizational Affiliation

    Research & Development, Bristol Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, United States. Electronic address: itr114@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1
A, B, C, D
406Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.882α = 90
b = 120.287β = 119.38
c = 100.821γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary