5YP5 | pdb_00005yp5

Crystal structure of RORgamma complexed with SRC2 and compound 5d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

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 4CZClick on this verticalbar to view details

This is version 1.1 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-gamma243Homo 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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SRC2-2 peptide8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4CZ
Query on 4CZ

Download Ideal Coordinates CCD File 
C [auth A]2-[4-(ethylsulfonyl)phenyl]-N-{5-[2-(2-methylpropyl)benzoyl]-4-phenyl-1,3-thiazol-2-yl}acetamide
C30 H30 N2 O4 S2
JCEZUYLHQPJLPN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4CZ BindingDB:  5YP5 IC50: 2.51e+4 (nM) from 1 assay(s)
EC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.069α = 90
b = 62.069β = 90
c = 154.818γ = 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 4CZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references