7JYM | pdb_00007jym

CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(244-487)-L6-SRC1(678-692)) IN COMPLEX WITH A TRICYCLIC SULFONE INVERSE AGONIST


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.264 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Novel Tricyclic Pyroglutamide Derivatives as Potent ROR gamma t Inverse Agonists Identified using a Virtual Screening Approach.

Liu, Q.Batt, D.G.Weigelt, C.A.Yip, S.Wu, D.R.Ruzanov, M.Sack, J.S.Wang, J.Yarde, M.Li, S.Shuster, D.J.Xie, J.H.Sherry, T.Obermeier, M.T.Fura, A.Stefanski, K.Cornelius, G.Khandelwal, P.Tino, J.A.Macor, J.E.Salter-Cid, L.Denton, R.Zhao, Q.Dhar, T.G.M.

(2020) ACS Med Chem Lett 11: 2510-2518

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00496
  • Primary Citation Related Structures: 
    7JYM

  • PubMed Abstract: 

    Employing a virtual screening approach, we identified the pyroglutamide moiety as a nonacid replacement for the cyclohexanecarboxylic acid group which, when coupled to our previously reported conformationally locked tricyclic core, provided potent and selective RORγt inverse agonists. Structure-activity relationship optimization of the pyroglutamide moiety led to the identification of compound 18 as a potent and selective RORγt inverse agonist, albeit with poor aqueous solubility. We took advantage of the tertiary carbinol group in 18 to synthesize a phosphate prodrug, which provided good solubility, excellent exposures in mouse PK studies, and significant efficacy in a mouse model of psoriasis.


  • Organizational Affiliation
    • Research and Early Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540-4000, United States.

Macromolecule Content 

  • Total Structure Weight: 33.59 kDa 
  • Atom Count: 2,108 
  • Modeled Residue Count: 253 
  • Deposited Residue Count: 285 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma, Nuclear receptor coactivator 1285Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRGNCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
GTEx:  ENSG00000143365 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
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
Z8I
(Subject of Investigation/LOI)

Query on Z8I



Download:Ideal Coordinates CCD File
B [auth A](3R,5S)-3-fluoro-5-[(3aR,9bR)-9b-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,2,3,3,3-heptafluoropropan-2-yl)-1,2,3a,4,5,9b-hexahydro-3H-benzo[e]indole-3-carbonyl]-1-(2-hydroxy-2-methylpropyl)pyrrolidin-2-one
C30 H29 F9 N2 O5 S
NETWYXYMXZLUOG-QSGNWFJVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z8I BindingDB:  7JYM EC50: min: 16, max: 43 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.264 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.297α = 90
b = 61.297β = 90
c = 155.945γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-11-25 
  • Deposition Author(s): Sack, J.

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description