6WJY

HUMAN IDO1 IN COMPLEX WITH COMPOUND 4-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent and Orally Available Bicyclo[1.1.1]pentane-Derived Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitors.

Pu, Q.Zhang, H.Guo, L.Cheng, M.Doty, A.C.Ferguson, H.Fradera, X.Lesburg, C.A.McGowan, M.A.Miller, J.R.Geda, P.Song, X.Otte, K.Sciammetta, N.Solban, N.Yu, W.Sloman, D.L.Zhou, H.Lammens, A.Neumann, L.Bennett, D.J.Pasternak, A.Han, Y.

(2020) ACS Med Chem Lett 11: 1548-1554

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00195
  • Primary Citation of Related Structures:  
    6WJY

  • PubMed Abstract: 

    Indoleamine-2,3-dioxygenase 1 (IDO1) inhibition and its combination with immune checkpoint inhibitors like pembrolizumab have drawn considerable attention from both academia and the pharmaceutical industry. Here, we describe the discovery of a novel class of highly potent IDO1 heme-displacing inhibitors featuring a unique bicyclo[1.1.1]pentane motif. Compound 1 , evolving from an ALIS (automated ligand identification system) hit, exhibited excellent potency but lacked the desired pharmacokinetic profile due to extensive amide hydrolysis of the benzamide moiety. Replacing the central phenyl ring in 1 with a bicyclo[1.1.1]pentane bioisostere effectively circumvented the amide hydrolysis issue, resulting in the discovery of compound 2 with a favorable overall profile such as excellent potency, selectivity, pharmacokinetics, and a low predicted human dose.


  • Organizational Affiliation

    Boston Discovery Chemistry, Therapeutic Modalities, Quantitative Biosciences, Discovery Pharm Science Boston/Westpoint, Computational & Structural Chemistry, Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co. Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U41 (Subject of Investigation/LOI)
Query on U41

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide
C21 H20 Cl F N2 O2
ORFXTXYARYWSKK-PZVFOTJXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U41 Binding MOAD:  6WJY IC50: 3.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.128α = 90
b = 91.433β = 90
c = 128.629γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Advisory, Data collection, Database references, Refinement description