6AZV

IDO1/BMS-978587 crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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:  
    6AZU, 6AZV, 6AZW

  • 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 catalyzes the oxidation of tryptophan to N -formylkynurenine ...

    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; jtgroves@princeton.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1A, B, C, D402Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C4V (Subject of Investigation/LOI)
Query on C4V

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D](1R,2S)-2-(4-[bis(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid
C26 H35 N3 O3
VZYCPKLOYXSKAB-FGZHOGPDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.392α = 90
b = 120.868β = 119.11
c = 101.527γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2017-09-13 
  • Released Date: 2018-03-21 
  • Deposition Author(s): Lewis, H.A.

Revision History  (Full details and data files)

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