4ZOM | pdb_00004zom

RORgamma in complex with inverse agonist 4j.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.240 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.202 (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 1.3 of the entry. See complete history

Literature

Discovery of novel pyrazole-containing benzamides as potent ROR gamma inverse agonists.

Wang, T.Banerjee, D.Bohnert, T.Chao, J.Enyedy, I.Fontenot, J.Guertin, K.Jones, H.Lin, E.Y.Marcotte, D.Talreja, T.Van Vloten, K.

(2015) Bioorg Med Chem Lett 25: 2985-2990

  • DOI: https://doi.org/10.1016/j.bmcl.2015.05.028
  • Primary Citation Related Structures: 
    4ZOM

  • PubMed Abstract: 

    The nuclear receptor RORγ plays a central role in controlling a pro-inflammatory gene expression program in several lymphocyte lineages including TH17 cells. RORγ-dependent inflammation has been implicated in the pathogenesis of several major autoimmune diseases and thus RORγ is an attractive target for therapeutic intervention in these diseases. Starting from a lead biaryl compound 4a, replacement of the head phenyl moiety with a substituted aminopyrazole group resulted in a series with improved physical properties. Further SAR exploration led to analogues (e.g., 4j and 5m) as potent RORγ inverse agonists.


  • Organizational Affiliation
    • Chemistry and Molecular Therapeutics, Biogen, 12 Cambridge Center, Cambridge, MA 02142, USA. Electronic address: taowang2@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 106.68 kDa 
  • Atom Count: 7,255 
  • Modeled Residue Count: 879 
  • Deposited Residue Count: 900 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B, C, D
225Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
UniProt & NIH Common Fund Data Resources
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 GroupP51449
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.240 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.422α = 90
b = 99.422β = 90
c = 129.439γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Data collection
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description