5YP6

RORgamma (263-509) complexed with SRC2 and Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

From ROR gamma t Agonist to Two Types of ROR gamma t Inverse Agonists

Wang, Y.Cai, W.Tang, T.Liu, Q.Yang, T.Yang, L.Ma, Y.Zhang, G.Huang, Y.Song, X.Orband-Miller, L.A.Wu, Q.Zhou, L.Xiang, Z.Xiang, J.N.Leung, S.Shao, L.Lin, X.Lobera, M.Ren, F.

(2018) ACS Med Chem Lett 9: 120-124

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00476
  • Primary Citation of Related Structures:  
    5YP5, 5YP6

  • PubMed Abstract: 

    Biaryl amides as new RORγt modulators were discovered. The crystal structure of biaryl amide agonist 6 in complex with RORγt ligand binding domain (LBD) was resolved, and both "short" and "long" inverse agonists were obtained by removing from 6 or adding to 6 a proper structural moiety. While "short" inverse agonist ( 8 ) recruits a corepressor peptide and dispels a coactivator peptide, "long" inverse agonist ( 9 ) dispels both. The two types of inverse agonists can be utilized as potential tools to study mechanisms of Th17 transcriptional network inhibition and related disease biology.


  • Organizational Affiliation

    School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma245Homo 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SRC28Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4CX (Subject of Investigation/LOI)
Query on 4CX

Download Ideal Coordinates CCD File 
C [auth A]N-[3'-cyano-4'-(2-methylpropyl)-2-(trifluoromethyl)biphenyl-4-yl]-2-[4-(ethylsulfonyl)phenyl]acetamide
C28 H27 F3 N2 O3 S
IDDOTRDVQFMFJR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4CX BindingDB:  5YP6 IC50: 2.51e+4 (nM) from 1 assay(s)
EC50: 20 (nM) from 1 assay(s)
Binding MOAD:  5YP6 IC50: 3.16e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.201α = 90
b = 62.201β = 90
c = 154.822γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description