5YP6 | pdb_00005yp6

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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4CXClick on this verticalbar to view details

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 
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 
Entity Groups  
UniProt GroupQ15788
Sequence Annotations
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  • 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)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4CXClick on this verticalbar to view details

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