6KPS

Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report



Literature

Unique Sulfur-Aromatic Interactions Contribute to the Binding of Potent Imidazothiazole Indoleamine 2,3-Dioxygenase Inhibitors.

Peng, Y.H.Liao, F.Y.Tseng, C.T.Kuppusamy, R.Li, A.S.Chen, C.H.Fan, Y.S.Wang, S.Y.Wu, M.H.Hsueh, C.C.Chang, J.Y.Lee, L.C.Shih, C.Shia, K.S.Yeh, T.K.Hung, M.S.Kuo, C.C.Song, J.S.Wu, S.Y.Ueng, S.H.

(2020) J Med Chem 63: 1642-1659

  • DOI: 10.1021/acs.jmedchem.9b01549
  • Primary Citation of Related Structures:  
    6KW7, 6KOF, 6KPS

  • PubMed Abstract: 
  • Indoleamine 2,3-dioxygenase (IDO1) inhibitors are speculated to be useful in cancer immunotherapy, but a phase III clinical trial of the most advanced IDO1 inhibitor, epacadostat, did not meet its primary end point and was abandoned. In previous work ...

    Indoleamine 2,3-dioxygenase (IDO1) inhibitors are speculated to be useful in cancer immunotherapy, but a phase III clinical trial of the most advanced IDO1 inhibitor, epacadostat, did not meet its primary end point and was abandoned. In previous work, we identified the novel IDO1 inhibitor N -(4-chlorophenyl)-2-((5-phenylthiazolo[2,3- c ][1,2,4]triazol-3-yl)thio)acetamide 1 through high-throughput screening (HTS). Herein, we report a structure-activity relationship (SAR) study of this compound, which resulted in the potent IDO1 inhibitor 1-(4-cyanophenyl)-3-(3-(cyclopropylethynyl)imidazo[2,1- b ]thiazol-5-yl)thiourea 47 (hIDO IC 50 = 16.4 nM). X-ray cocrystal structural analysis revealed that the basis for this high potency is a unique sulfur-aromatic interaction network formed by the thiourea moiety of 47 with F163 and F226. This finding is expected to inspire new approaches toward the discovery of potent IDO1 inhibitors in the future.


    Organizational Affiliation

    School of Pharmacy , National Cheng Kung University , Tainan 70101 , Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1A, B403Homo sapiensMutation(s): 0 
Gene Names: IDO1IDOINDO
EC: 1.13.11.52
Find proteins for P14902 (Homo sapiens)
Explore P14902 
Go to UniProtKB:  P14902
NIH Common Fund Data Resources
PHAROS  P14902
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DU6
Query on DU6

Download CCD File 
A, B
1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]urea
C19 H15 N5 O S
JCNMORLJVKCDDB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.693α = 90
b = 92.555β = 90
c = 130.661γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-08-16 
  • Released Date: 2020-03-25 
  • Deposition Author(s): Peng, Y.H., Wu, S.Y.

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release