6AZW

IDO1/FXB-001116 crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form.

Nelp, M.T.Kates, P.A.Hunt, J.T.Newitt, J.A.Balog, A.Maley, D.Zhu, X.Abell, L.Allentoff, A.Borzilleri, R.Lewis, H.A.Lin, Z.Seitz, S.P.Yan, C.Groves, J.T.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 3249-3254

  • DOI: 10.1073/pnas.1719190115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For cancer cells to survive and proliferate, they must escape normal immune destruction. One mechanism by which this is accomplished is through immune suppression effected by up-regulation of indoleamine 2,3-dioxygenase (IDO1), a heme enzyme that cat ...

    For cancer cells to survive and proliferate, they must escape normal immune destruction. One mechanism by which this is accomplished is through immune suppression effected by up-regulation of indoleamine 2,3-dioxygenase (IDO1), a heme enzyme that catalyzes the oxidation of tryptophan to N -formylkynurenine. On deformylation, kynurenine and downstream metabolites suppress T cell function. The importance of this immunosuppressive mechanism has spurred intense interest in the development of clinical IDO1 inhibitors. Herein, we describe the mechanism by which a class of compounds effectively and specifically inhibits IDO1 by targeting its apo-form. We show that the in vitro kinetics of inhibition coincide with an unusually high rate of intrinsic enzyme-heme dissociation, especially in the ferric form. X-ray crystal structures of the inhibitor-enzyme complexes show that heme is displaced from the enzyme and blocked from rebinding by these compounds. The results reveal that apo-IDO1 serves as a unique target for inhibition and that heme lability plays an important role in posttranslational regulation.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ 08544.,Leads Discovery and Optimization, Bristol-Myers Squibb Co., Princeton, NJ 08543.,Immuno-oncology Biology, Bristol-Myers Squibb Co., Princeton, NJ 08543.,Department of Radiochemistry, Bristol-Myers Squibb Co., Princeton, NJ 08543.,Department of Chemistry, Princeton University, Princeton, NJ 08544; jtgroves@princeton.edu.,Molecular Discovery Technologies, Bristol-Myers Squibb Co., Princeton, NJ 08543.,Department of Discovery Chemistry, Bristol-Myers Squibb Co., Princeton, NJ 08543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Indoleamine 2,3-dioxygenase 1
A, B
394Homo sapiensMutation(s): 0 
Gene Names: IDO1 (IDO, INDO)
EC: 1.13.11.52
Find proteins for P14902 (Homo sapiens)
Go to Gene View: IDO1
Go to UniProtKB:  P14902
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C51
Query on C51

Download SDF File 
Download CCD File 
A, B
(2R)-N-(4-cyanophenyl)-2-[cis-4-(quinolin-4-yl)cyclohexyl]propanamide
C25 H25 N3 O
GDSGPUWADCUKPY-RLLQIKCJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.206α = 90.00
b = 92.555β = 90.00
c = 128.698γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references