5NI8

Ligand complex of RORg LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent and Orally Bioavailable Inverse Agonists of ROR gamma t Resulting from Structure-Based Design.

Narjes, F.Xue, Y.von Berg, S.Malmberg, J.Llinas, A.Olsson, R.I.Jirholt, J.Grindebacke, H.Leffler, A.Hossain, N.Lepisto, M.Thunberg, L.Leek, H.Aagaard, A.McPheat, J.Hansson, E.L.Back, E.Tangefjord, S.Chen, R.Xiong, Y.Hongbin, G.Hansson, T.G.

(2018) J Med Chem 61: 7796-7813

  • DOI: 10.1021/acs.jmedchem.8b00783
  • Primary Citation of Related Structures:  
    6ESN, 6FGQ, 5NIB, 5NI8, 5NI5, 5NI7

  • PubMed Abstract: 
  • Retinoic acid receptor related orphan receptor γt (RORγt), has been identified as the master regulator of T H 17-cell function and development, making it an attractive target for the treatment of autoimmune diseases by a small-molecule approach ...

    Retinoic acid receptor related orphan receptor γt (RORγt), has been identified as the master regulator of T H 17-cell function and development, making it an attractive target for the treatment of autoimmune diseases by a small-molecule approach. Herein, we describe our investigations on a series of 4-aryl-thienyl acetamides, which were guided by insights from X-ray cocrystal structures. Efforts in targeting the cofactor-recruitment site from the 4-aryl group on the thiophene led to a series of potent binders with nanomolar activity in a primary human-T H 17-cell assay. The observation of a DMSO molecule binding in a subpocket outside the LBD inspired the introduction of an acetamide into the benzylic position of these compounds. Hereby, a hydrogen-bond interaction of the introduced acetamide oxygen with the backbone amide of Glu379 was established. This greatly enhanced the cellular activity of previously weakly cell-active compounds. The best compounds combined potent inhibition of IL-17 release with favorable PK in rodents, with compound 32 representing a promising starting point for future investigations.


    Organizational Affiliation

    Pharmaron Beijing Company, Ltd. , Taihe Road , BDA, Beijing 100176 , PR China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA288Homo 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
The Tethered SRC2-2 peptideB [auth C]15Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Y2
Query on 8Y2

Download Ideal Coordinates CCD File 
C [auth A]2-(4-ethylsulfonylphenyl)-~{N}-[4-(2-phenylmethoxypyridin-3-yl)thiophen-2-yl]ethanamide
C26 H24 N2 O4 S2
RHPSXPWLHPRNOB-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8Y2IC50:  20   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.15α = 90
b = 62.15β = 90
c = 158.31γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references