5ETW

Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1.

Peng, Y.H.Ueng, S.H.Tseng, C.T.Hung, M.S.Song, J.S.Wu, J.S.Liao, F.Y.Fan, Y.S.Wu, M.H.Hsiao, W.C.Hsueh, C.C.Lin, S.Y.Cheng, C.Y.Tu, C.H.Lee, L.C.Cheng, M.F.Shia, K.S.Shih, C.Wu, S.Y.

(2016) J.Med.Chem. 59: 282-293

  • DOI: 10.1021/acs.jmedchem.5b01390
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Indoleamine 2,3-dioxygenase 1 (IDO1), promoting immune escape of tumors, is a therapeutic target for the cancer immunotherapy. A number of IDO1 inhibitors have been identified, but only limited structural biology studies of IDO1 inhibitors are availa ...

    Indoleamine 2,3-dioxygenase 1 (IDO1), promoting immune escape of tumors, is a therapeutic target for the cancer immunotherapy. A number of IDO1 inhibitors have been identified, but only limited structural biology studies of IDO1 inhibitors are available to provide insights on the binding mechanism of IDO1. In this study, we present the structure of IDO1 in complex with 24, a NLG919 analogue with potent activity. The complex structure revealed the imidazole nitrogen atom of 24 to coordinate with the heme iron, and the imidazoleisoindole core situated in pocket A with the 1-cyclohexylethanol moiety extended to pocket B to interact with the surrounding residues. Most interestingly, 24 formed an extensive hydrogen bond network with IDO1, which is a distinct feature of IDO1/24 complex structure and is not observed in the other IDO1 complex structures. Further structure-activity relationship, UV spectra, and structural biology studies of several analogues of 24 demonstrated that extensive hydrophobic interactions and the unique hydrogen bonding network contribute to the great potency of imidazoleisoindole derivatives. These results are expected to facilitate the structure-based drug design of new IDO inhibitors.


    Organizational Affiliation

    Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Indoleamine 2,3-dioxygenase 1
A, B
403Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XNL
Query on XNL

Download SDF File 
Download CCD File 
A, B
(1~{R})-1-cyclohexyl-2-pyrido[3,4-b]indol-9-yl-ethanol
C19 H22 N2 O
MMCCSFCZNUXGJD-IBGZPJMESA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XNLIC50: 48000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.674α = 90.00
b = 91.432β = 90.00
c = 128.373γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Data collection, Database references, Derived calculations