6V52 | pdb_00006v52

IDO1 IN COMPLEX WITH COMPOUND 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.220 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6V52

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Strategic Incorporation of Polarity in Heme-Displacing Inhibitors of Indoleamine-2,3-dioxygenase-1 (IDO1).

White, C.McGowan, M.A.Zhou, H.Sciammetta, N.Fradera, X.Lim, J.Joshi, E.M.Andrews, C.Nickbarg, E.B.Cowley, P.Trewick, S.Augustin, M.von Koenig, K.Lesburg, C.A.Otte, K.Knemeyer, I.Woo, H.Yu, W.Cheng, M.Spacciapoli, P.Geda, P.Song, X.Smotrov, N.Curran, P.Heo, M.R.Abeywickrema, P.Miller, J.R.Bennett, D.J.Han, Y.

(2020) ACS Med Chem Lett 11: 550-557

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00010
  • Primary Citation Related Structures: 
    6V52

  • PubMed Abstract: 

    Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as a target of significant interest to the field of cancer immunotherapy, as the upregulation of IDO1 in certain cancers has been linked to host immune evasion and poor prognosis for patients. In particular, IDO1 inhibition is of interest as a combination therapy with immune checkpoint inhibition. Through an Automated Ligand Identification System (ALIS) screen, a diamide class of compounds was identified as a promising lead for the inhibition of IDO1. While hit 1 possessed attractive cell-based potency, it suffered from a significant right-shift in a whole blood assay, poor solubility, and poor pharmacokinetic properties. Through a physicochemical property-based approach, including a focus on lowering AlogP 98 via the strategic introduction of polar substitution, compound 13 was identified bearing a pyridyl oxetane core. Compound 13 demonstrated improved whole blood potency and solubility, and an improved pharmacokinetic profile resulting in a low predicted human dose.


  • Organizational Affiliation
    • Department of Chemistry, Computational and Structural Chemistry, Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Quantitative Biosciences, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

Macromolecule Content 

  • Total Structure Weight: 89.45 kDa 
  • Atom Count: 6,672 
  • Modeled Residue Count: 753 
  • Deposited Residue Count: 788 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1
A, B
394Homo 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
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
QPV BindingDB:  6V52 IC50: min: 9, max: 22 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.245α = 90
b = 90.448β = 90
c = 130.034γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Advisory, Data collection, Database references, Structure summary