6O3I

Crystal Structure of Human IDO1 bound to navoximod (NLG-919)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Clinical Candidate (1R,4r)-4-((R)-2-((S)-6-Fluoro-5H-imidazo[5,1-a]isoindol-5-yl)-1-hydroxyethyl)cyclohexan-1-ol (Navoximod), a Potent and Selective Inhibitor of Indoleamine 2,3-Dioxygenase 1.

Kumar, S.Waldo, J.P.Jaipuri, F.A.Marcinowicz, A.Van Allen, C.Adams, J.Kesharwani, T.Zhang, X.Metz, R.Oh, A.J.Harris, S.F.Mautino, M.R.

(2019) J Med Chem 62: 6705-6733

  • DOI: 10.1021/acs.jmedchem.9b00662
  • Primary Citation of Related Structures:  
    6O3I

  • PubMed Abstract: 
  • A novel class of 5-substituted 5 H -imidazo[5,1- a ]isoindoles are described as potent inhibitors of indoleamine 2,3-dioxygenase 1 (IDO1). A structure-based drug design approach was used to elaborate the 5 H -imidazo[5,1- a ]isoindole core and to improve potency and pharmacological properties ...

    A novel class of 5-substituted 5 H -imidazo[5,1- a ]isoindoles are described as potent inhibitors of indoleamine 2,3-dioxygenase 1 (IDO1). A structure-based drug design approach was used to elaborate the 5 H -imidazo[5,1- a ]isoindole core and to improve potency and pharmacological properties. Suitably placed hydrophobic and polar functional groups in the lead molecule allowed improvement of IDO1 inhibitory activity while minimizing off-target liabilities. Structure-activity relationship studies focused on optimizing IDO1 inhibition potency and a pharmacokinetic profile amenable to oral dosing while controlling CYP450 and hERG inhibitory properties.


    Organizational Affiliation

    NewLink Genetics Corporation , Ames , Iowa 50010 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1A, B420Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14902
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LKP (Subject of Investigation/LOI)
Query on LKP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
trans-4-{(1R)-2-[(5S)-6-fluoro-5H-imidazo[5,1-a]isoindol-5-yl]-1-hydroxyethyl}cyclohexan-1-ol
C18 H21 F N2 O2
YGACXVRLDHEXKY-WXRXAMBDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LKP BindingDB:  6O3I Ki: 5.8 (nM) from 1 assay(s)
IC50: min: 13, max: 1000 (nM) from 8 assay(s)
EC50: min: 75, max: 250 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.062α = 90
b = 90.224β = 90
c = 130.237γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
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: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references