7JTW | pdb_00007jtw

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 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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 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].
Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan.
Department of Medicinal Chemistry, Amgen Discovery Research, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States.
Departments of Molecular Engineering, Amgen Discovery Research, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, United States.
Departments of Inflammation & Oncology Research Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, United States.
AMRI Singapore Research Centre, Pte. Ltd., 61 Science Park Road, #05-01 The Galen, Science Park III, Singapore 117525, Singapore.
Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, 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 
• Modeled 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 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

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