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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YP6

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 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.

Macromolecule Content 

  • Total Structure Weight: 30.09 kDa 
  • Atom Count: 2,131 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 253 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.213 (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 


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