6B33

Structure of RORgt in complex with a novel inverse agonist 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of Conformationally Constrained ROR gamma t Inverse Agonists.

Sato, A.Fukase, Y.Kono, M.Ochida, A.Oda, T.Sasaki, Y.Ishii, N.Tomata, Y.Fukumoto, S.Imai, Y.N.Uga, K.Shibata, A.Yamasaki, M.Nakagawa, H.Shirasaki, M.Skene, R.Hoffman, I.Sang, B.C.Snell, G.Shirai, J.Yamamoto, S.

(2019) ChemMedChem 

  • DOI: https://doi.org/10.1002/cmdc.201900416
  • Primary Citation of Related Structures:  
    6B33

  • PubMed Abstract: 

    Retinoic-acid-related orphan receptor γt (RORγt) inverse agonists could be used for the treatment of autoimmune diseases. Previously, we reported a novel quinazolinedione 1 a with a flexible linear linker as a novel RORγt inverse agonist. A U-shaped conformation in the complex structure of 1 a with RORγt protein was confirmed. Further improvement of the pharmacokinetic (PK) profiles was required because of the low drug exposure in mice upon oral administration (mouse AUC of 1 a: 27 ng ⋅ h ⋅ mL -1 at 1 mg ⋅ kg -1 , p.o.). To improve the PK profiles, conformationally constrained U-shaped scaffolds were investigated. As a result, morpholine analogues with improved PK profiles and high potency were successfully identified. The substituent at the N1 position of the quinazoline moiety was also modified, leading to an enhancement of reporter activity. Consequently, compound 43 (N 2 -(3-chloro-4-cyanophenyl)-N 4 -(3-(cyclopropylmethyl)-1-isopropyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-6-yl)morpholine-2,4-dicarboxamide) exhibited improved drug exposure (mouse AUC: 1289 ng ⋅ h ⋅ mL -1 at 1 mg ⋅ kg -1 , p.o.). In addition, suppression of IL-17A gene expression by IL-23 stimulation in a mouse pharmacodynamics model was observed for 43. The conformation of 43 with RORγt protein was also confirmed as U-shape by X-ray co-crystal structure analysis. The key interaction that boosts potency is also discussed.


  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraokahigashi 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
218Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CF7 (Subject of Investigation/LOI)
Query on CF7

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2R)-N~2~-(3-chloro-4-cyanophenyl)-N~4~-[3-(cyclopropylmethyl)-2,4-dioxo-1-(propan-2-yl)-1,2,3,4-tetrahydroquinazolin-6-yl]morpholine-2,4-dicarboxamide
C28 H29 Cl N6 O5
QUTSLTZISBFEOJ-XMMPIXPASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CF7 BindingDB:  6B33 IC50: 3.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.211α = 90
b = 99.211β = 90
c = 126.332γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references