6W9I

SUBSTITUTED BENZYLOXYTRICYCLIC COMPOUNDS AS RETINOIC ACID-RELATED ORPHAN RECEPTOR GAMMA T AGONISTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substituted benzyloxytricyclic compounds as retinoic acid-related orphan receptor gamma t (ROR gamma t) agonists.

Harikrishnan, L.S.Gill, P.Kamau, M.G.Qin, L.Y.Ruan, Z.O'Malley, D.Huynh, T.Stachura, S.Cavallaro, C.L.Lu, Z.J-W Duan, J.Weigelt, C.A.Sack, J.S.Ruzanov, M.Khan, J.Gururajan, M.Wong, J.J.Huang, Y.Yarde, M.Li, Z.Chen, C.Sun, H.Borowski, V.Murtaza, A.Fink, B.E.

(2020) Bioorg Med Chem Lett 30: 127204-127204

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127204
  • Primary Citation of Related Structures:  
    6W9H, 6W9I, 6XAE

  • PubMed Abstract: 

    Substituted benzyloxy aryl compound 2 was identified as an RORγt agonist. Structure based drug design efforts resulted in a potent and selective tricyclic compound 19 which, when administered orally in an MC38 mouse tumor model, demonstrated a desired pharmacokinetic profile as well as a dose-dependent pharmacodynamic response. However, no perceptible efficacy was observed in this tumor model at the doses investigated.


  • Organizational Affiliation

    Department of Chemistry, Bristol Myers Squibb Company, P.O. Box 4000, Princeton, NJ, USA. Electronic address: lalgudi.harikrishnan@bms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma, Steroid receptor coactivator 1 fusion285Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRGNCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15788P51449
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z7D (Subject of Investigation/LOI)
Query on Z7D

Download Ideal Coordinates CCD File 
B [auth A]1-(benzyloxy)-4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}benzene
C24 H23 F O3 S
IXMWLTXJOWOLAW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z7D BindingDB:  6W9I EC50: 214 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.681α = 90
b = 61.681β = 90
c = 155.162γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-04-29 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description