8I7L

Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Apo-Form Selective Inhibition of IDO for Tumor Immunotherapy.

Liu, W.Zou, Y.Li, K.Zhong, H.Yu, L.Ge, S.Lai, Y.Dong, X.Xu, Q.Guo, W.

(2022) J Immunol 209: 180-191

  • DOI: https://doi.org/10.4049/jimmunol.2100938
  • Primary Citation of Related Structures:  
    8I7L

  • PubMed Abstract: 

    The pharmacological inhibition of IDO1 is considered an effective therapeutic approach for cancer treatment. However, the inadequate response of existing holo-IDO1 inhibitors and unclear biomarkers available in clinical practice limit the possibility of developing efficacious IDO1 inhibitors. In the current study, we aimed to elucidate the activity and mechanism of a potent 1 H -pyrrole-2-carboxylic acid derivative (B37) targeting apo-IDO1 and to determine its role in tumor therapy. By competing with heme for binding to apo-IDO1, B37 potently inhibited IDO1 activity, with an IC 50 of 22 pM assessed using a HeLa cell-based assay. The x-ray cocrystal structure of the inhibitor-enzyme complex showed that the B37-human IDO1 complex has strong hydrophobic interactions, which enhances its binding affinity, determined using isothermal titration calorimetry. Stronger noncovalent interactions, including π stacking and hydrogen bonds formed between B37 and apo-human IDO1, underlay the enthalpy-driven force for B37 for binding to the enzyme. These binding properties endowed B37 with potent antitumor efficacy, which was confirmed in a mouse colon cancer CT26 syngeneic model in BALB/c mice and in an azoxymethane/dextran sulfate sodium-induced colon carcinogenesis model in C57BL/6 mice by activating the host immune system. Moreover, the combination of B37 and anti-PD1 Ab synergistically inhibited tumor growth. These results suggested that B37 may serve as a unique candidate for apo-IDO1 inhibition-mediated tumor immunotherapy.


  • Organizational Affiliation

    State Key Laboratory of Pharmaceutical Biotechnology, Engineering Research Center of Protein and Peptide Medicine, School of Life Sciences, Nanjing University, Nanjing, People's Republic of China; and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1
A, B
403Homo 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
GTEx:  ENSG00000131203 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14902
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OIH (Subject of Investigation/LOI)
Query on OIH

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
1-[3-[(4-chloranyl-2-fluoranyl-phenyl)carbamoylamino]-4-[cyclohexyl(2-methylpropyl)amino]phenyl]pyrrole-2-carboxylic acid
C28 H32 Cl F N4 O3
JYDXSLBOQXZAKM-UHFFFAOYSA-N
THJ
Query on THJ

Download Ideal Coordinates CCD File 
C [auth A]THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.11α = 90
b = 97.11β = 90
c = 128.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81922067
National Natural Science Foundation of China (NSFC)China21937005
National Natural Science Foundation of China (NSFC)China21772233
National Natural Science Foundation of China (NSFC)China81903620

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references