6W9H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma, Steroid receptor coactivator 1 fusionA285Homo 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 GroupsP51449Q15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TKJ (Subject of Investigation/LOI)
Query on TKJ

Download Ideal Coordinates CCD File 
B [auth A]4-{(3R)-3-[4-(benzyloxy)phenyl]-3-[(4-fluorophenyl)sulfonyl]pyrrolidine-1-carbonyl}-1lambda~6~-thiane-1,1-dione
C29 H30 F N O6 S2
GHRPDEFVTTUXKB-LJAQVGFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.729α = 90
b = 61.729β = 90
c = 155.778γ = 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

  • Deposited Date: 2020-03-23 
  • 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