7JTW

Crystal structure of RORgt with compound (4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid

• PDB DOI: https://doi.org/10.2210/pdb7JTW/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-08-18 Released: 2021-02-03 
• Deposition Author(s): Min, X., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Discovery of 6-Oxo-4-phenyl-hexanoic acid derivatives as ROR gamma t inverse agonists showing favorable ADME profile.

Nakajima, R., Oono, H., Kumazawa, K., Ida, T., Hirata, J., White, R.D., Min, X., Guzman-Perez, A., Wang, Z., Symons, A., Singh, S.K., Mothe, S.R., Belyakov, S., Chakrabarti, A., Shuto, S.

(2021) Bioorg Med Chem Lett 36: 127786-127786

• PubMed: 33493627 
• DOI: https://doi.org/10.1016/j.bmcl.2021.127786
• Primary Citation of Related Structures:  
  7JTW


• PubMed Abstract: 
  

  The retinoic acid receptor-related orphan nuclear receptor gamma t (RORγt), which is a promising therapeutic target for immune diseases, is a major transcription factor of genes related to psoriasis pathogenesis, such as interleukin (IL)-17A, IL-22, and IL-23R. Inspired by the co-crystal structure of RORγt, a 6-oxo-4-phenyl-hexanoic acid derivative 6a was designed, synthesized, and identified as a ligand of RORγt. The structure-activity relationship (SAR) studies in 6a, which focus on the improvement of its membrane permeability profile by introducing chlorine atoms, led to finding 12a, which has a potent RORγt inhibitory activity and a favorable pharmacokinetic profile.

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Organizational Affiliation: 

Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.15 kDa 
• Atom Count: 2,290 
• Modelled Residue Count: 259 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAR-related orphan receptor C isoform a variant	A	270	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449  Go to UniProtKB:  P51449
PHAROS:  P51449 GTEx:  ENSG00000143365

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VK4 (Subject of Investigation/LOI)	B [auth A]	(4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid C30 H36 Cl2 N2 O5 NWXXXIQTJWEGQR-ZFJSRUIDSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.991	α = 90
b = 61.991	β = 90
c = 156.838	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Min, X., Wang, Z.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2021-02-17
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description