6FGQ

Ligand complex of RORg LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5NI5, 5NI7, 5NI8, 5NIB, 6ESN, 6FGQ

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA, B265Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D9N
Query on D9N

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl 4-[[3-[5-[2-(4-ethylsulfonylphenyl)ethanoylamino]thiophen-3-yl]pyridin-2-yl]oxymethyl]benzoate
C28 H26 N2 O6 S2
QOZJVJXEWQEQGR-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
D9N BindingDB:  6FGQ IC50: min: 14, max: 35 (nM) from 3 assay(s)
Binding MOAD:  6FGQ IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.55α = 90
b = 99.55β = 90
c = 129.51γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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