9VNX | pdb_00009vnx

Crystal Structure of the mutant ROR gamma LBD With Compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Concise and Modular Approach to Generate Novel ROR gamma Agonists.

Fukuda, S.Ikenogami, T.Otake, K.Miwa, S.Maeda, K.Yamashita, T.Inami, T.Yokota, M.Lu, Y.Suma, A.Hirono, Y.Ogawa, N.Inoue, T.Harada, K.Yamaguchi, K.Akai, S.Nomura, A.Adachi, T.Terawaki, T.Suzukawa, A.Kitamoto, M.Tanimoto, M.Noguchi, T.Hata, T.Kawahara, I.Iwamoto, K.Kondo, K.Kitagawa, Y.Naka, Y.Crowe, P.Tao, H.Fenn, M.Thacher, S.Oba, M.Shiozaki, M.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00872
  • Primary Citation of Related Structures:  
    9VNX

  • PubMed Abstract: 

    A variety of RORγ inhibitors have been identified, including clinical compounds such as VTP-43742 and JTE-151. In contrast, RORγ agonists have been less explored and LYC-55716 is, to the best of our knowledge, the sole example reached a human clinical investigation. To generate a novel RORγ agonist, functionality switching from preceding RORγ inhibitors has been considered as a rational strategy. Such reported earlier attempts have been hampered by a loss of physicochemical properties to elevated lipophilicity. Starting from RORγ inhibitors, corresponding agonists were generated virtually to assess their druglike characters. Based on their ligand efficiency and lipophilicity, a cyclic amine carboxylate core was regarded as the best for maintaining favorable physicochemical properties. This scaffold was subjected to final optimization by attaching function-oriented modules retaining druglike properties. After multiparameter optimization, novel selective RORγ agonists were discovered, and their in vivo effects were confirmed in a syngeneic mouse model after oral administration.


  • Organizational Affiliation

    Central Pharmaceutical Research Institute, Takatsuki Research Center, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma258Homo sapiensMutation(s): 2 
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
Nuclear receptor coactivator 115Homo 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.664α = 90
b = 61.664β = 90
c = 155.779γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release