6E43

Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) in complex with a BMS-978587 analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form.

Luo, S.Xu, K.Xiang, S.Chen, J.Chen, C.Guo, C.Tong, Y.Tong, L.

(2018) Acta Crystallogr F Struct Biol Commun 74: 717-724

  • DOI: 10.1107/S2053230X18012955
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various i ...

    Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2-2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Indoleamine 2,3-dioxygenase 1
A, B, C, D
405Homo sapiensMutation(s): 2 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B, C, D
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
HQM
Query on HQM

Download SDF File 
Download CCD File 
A, B, C, D
(1R,2S)-2-(4-[cyclohexyl(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid
C28 H37 N3 O3
AHNMZQOTEVUTJH-DNQXCXABSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.481α = 90.00
b = 195.388β = 90.00
c = 118.223γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-07-16 
  • Released Date: 2018-11-14 
  • Deposition Author(s): Luo, S., Tong, L.

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release