6W9I

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

• PDB DOI: https://doi.org/10.2210/pdb6W9I/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-23 Released: 2020-04-29 
• Deposition Author(s): Sack, J.S.

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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

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

• PubMed: 32334911 
• 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.

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Organizational Affiliation: 

Department of Chemistry, Bristol Myers Squibb Company, P.O. Box 4000, Princeton, NJ, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.3 kDa 
• Atom Count: 2,301 
• Modelled Residue Count: 253 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma, Steroid receptor coactivator 1 fusion	A	285	Homo sapiens	Mutation(s): 0  Gene Names: RORC, NR1F3, RORG, RZRG, NCOA1, BHLHE74, SRC1 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
UniProt Groups	Q15788P51449

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z7D (Subject of Investigation/LOI)	B [auth A]	1-(benzyloxy)-4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}benzene C24 H23 F O3 S IXMWLTXJOWOLAW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 61.681	α = 90
b = 61.681	β = 90
c = 155.162	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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