6E3E | pdb_00006e3e

Structure of RORgt in complex with a novel inverse agonist.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (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 HQ7Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Biological Evaluation of Retinoic Acid-Related Orphan Receptor gamma t (ROR gamma t) Agonist Structure-Based Functionality Switching Approach from In House ROR gamma t Inverse Agonist to ROR gamma t Agonist.

Yukawa, T.Nara, Y.Kono, M.Sato, A.Oda, T.Takagi, T.Sato, T.Banno, Y.Taya, N.Imada, T.Shiokawa, Z.Negoro, N.Kawamoto, T.Koyama, R.Uchiyama, N.Skene, R.Hoffman, I.Chen, C.H.Sang, B.Snell, G.Katsuyama, R.Yamamoto, S.Shirai, J.

(2019) J Med Chem 62: 1167-1179

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01181
  • Primary Citation of Related Structures:  
    6E3E, 6E3G

  • PubMed Abstract: 

    Retinoic acid receptor-related orphan receptor γt (RORγt) agonists are expected to provide a novel class of immune-activating anticancer drugs via activation of Th17 cells and Tc17 cells. Herein, we describe a novel structure-based functionality switching approach from in house well-optimized RORγt inverse agonists to potent RORγt agonists. We succeeded in the identification of potent RORγt agonist 5 without major chemical structure change. The biochemical response was validated by molecular dynamics simulation studies that showed a helix 12 stabilization effect of RORγt agonists. These results indicate that targeting helix 12 is an attractive and novel medicinal chemistry strategy for switching existing RORγt inverse agonists to agonists.


  • Organizational Affiliation

    Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
217Homo 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HQ7
Query on HQ7

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
5-[(5R)-5-[(7-fluoro-1,1-dimethyl-2,3-dihydro-1H-inden-5-yl)carbamoyl]-2-methoxy-7,8-dihydro-1,6-naphthyridin-6(5H)-yl]-5-oxopentanoic acid
C26 H30 F N3 O5
BENOEPUDOPGLCP-XMMPIXPASA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.661α = 90
b = 99.661β = 90
c = 125.28γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

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 HQ7Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references