7RRC | pdb_00007rrc

IDO1 IN COMPLEX WITH COMPOUND 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.217 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7RRC

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Oxetane Promise Delivered: Discovery of Long-Acting IDO1 Inhibitors Suitable for Q3W Oral or Parenteral Dosing.

Li, D.Sloman, D.L.Achab, A.Zhou, H.McGowan, M.A.White, C.Gibeau, C.Zhang, H.Pu, Q.Bharathan, I.Hopkins, B.Liu, K.Ferguson, H.Fradera, X.Lesburg, C.A.Martinot, T.A.Qi, J.Song, Z.J.Yin, J.Zhang, H.Song, L.Wan, B.DAddio, S.Solban, N.Miller, J.R.Zamlynny, B.Bass, A.Freeland, E.Ykoruk, B.Hilliard, C.Ferraro, J.Zhai, J.Knemeyer, I.Otte, K.M.Vincent, S.Sciammetta, N.Pasternak, A.Bennett, D.J.Han, Y.

(2022) J Med Chem 65: 6001-6016

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01670
  • Primary Citation Related Structures: 
    7RRB, 7RRC

  • PubMed Abstract: 

    3,3-Disubstituted oxetanes have been utilized as bioisosteres for gem-dimethyl and cyclobutane functionalities. We report the discovery of a novel class of oxetane indole-amine 2,3-dioxygenase (IDO1) inhibitors suitable for Q3W (once every 3 weeks) oral and parenteral dosing. A diamide class of IDO inhibitors was discovered through an automated ligand identification system (ALIS). Installation of an oxetane and fluorophenyl dramatically improved the potency. Identification of a biaryl moiety as an unconventional amide isostere addressed the metabolic liability of amide hydrolysis. Metabolism identification (Met-ID)-guided target design and the introduction of polarity resulted in the discovery of potent IDO inhibitors with excellent pharmacokinetic (PK) profiles in multiple species. To enable rapid synthesis of the key oxetane intermediate, a novel oxetane ring cyclization was also developed, as well as optimization of a literature route on kg scale. These IDO inhibitors may enable unambiguous proof-of-concept testing for the IDO1 inhibition mechanism for oncology.


  • Organizational Affiliation
    • Pharmaron Beijing Co., Ltd., No.6 Taihe Road, Beijing 100176, China.

Macromolecule Content 

  • Total Structure Weight: 89.6 kDa 
  • Atom Count: 6,280 
  • Modeled Residue Count: 749 
  • 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

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6RI
(Subject of Investigation/LOI)

Query on 6RI



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N-(4-fluorophenyl)-3-{4-[4-(hydroxymethyl)-6-(trifluoromethyl)pyridin-3-yl]phenyl}oxetane-3-carboxamide
C23 H18 F4 N2 O3
KTZHBUHZJXHRMG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.217 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.95α = 90
b = 91.339β = 90
c = 129.223γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary