4XT9 | pdb_00004xt9

RORgamma (263-509) complexed with GSK2435341A and SRC2

• PDB DOI: https://doi.org/10.2210/pdb4XT9/pdb

• Classification: Unknown protein
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2015-01-23 Released: 2015-08-12 
• Deposition Author(s): Wang, Y., Ma, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.245 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Discovery of N-(4-aryl-5-aryloxy-thiazol-2-yl)-amides as potent ROR gamma t inverse agonists

Wang, Y., Yang, T., Liu, Q., Ma, Y., Yang, L., Zhou, L., Xiang, Z., Cheng, Z., Lu, S., Orband-Miller, L.A., Zhang, W., Wu, Q., Zhang, K., Li, Y., Xiang, J.N., Elliott, J.D., Leung, S., Ren, F., Lin, X.

(2015) Bioorg Med Chem 23: 5293-5302

• PubMed: 26277758 
• DOI: https://doi.org/10.1016/j.bmc.2015.07.068
• Primary Citation Related Structures: 
  4XT9


• PubMed Abstract: 
  

  A novel series of N-(4-aryl-5-aryloxy-thiazol-2-yl)-amides as RORγt inverse agonists was discovered. Binding mode analysis of a RORγt partial agonist (2c) revealed by co-crystal structure in RORγt LBD suggests that the inverse agonists do not directly interfere with the interaction between H12 and the RORγt LBD. Detailed SAR exploration led to identification of potent RORγt inverse agonists such as 3m with a pIC50 of 8.0. Selected compounds in the series showed reasonable activity in Th17 cell differentiation assay as well as low intrinsic clearance in mouse liver microsomes.

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Organizational Affiliation: 
• School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong, Shanghai 201203, China. Electronic address: [e-mail].
Research and Development, GlaxoSmithKline, No. 3 Building, 898 Halei Road, Pudong, Shanghai 201203, China.
Research and Development, GlaxoSmithKline, No. 3 Building, 898 Halei Road, Pudong, Shanghai 201203, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 30.05 kDa 
• Atom Count: 2,132 
• Modeled Residue Count: 251 
• Deposited Residue Count: 251 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A	243	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN	B	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
43V	C [auth A]	N-[4-(2,5-dichlorophenyl)-5-phenyl-1,3-thiazol-2-yl]-2-[4-(ethylsulfonyl)phenyl]acetamide C25 H20 Cl2 N2 O3 S2 NUQYLKJMFVEWEU-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.245 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62	α = 90
b = 62	β = 90
c = 154.7	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Wang, Y., Ma, Y.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description