5NI5

Ligand complex of RORg LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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

    Early Product Development , Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca , Gothenburg , SE-43183 Mölndal , Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma288Homo 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
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tethered SRC2-2 peptideB [auth C]15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8YB
Query on 8YB

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[4-(3-chlorophenyl)-5-(2-chlorophenyl)carbonyl-1,3-thiazol-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide
C26 H20 Cl2 N2 O4 S2
GRWNPFJXINLSNF-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8YB BindingDB:  5NI5 Ki: 40 (nM) from 1 assay(s)
IC50: min: 7.9, max: 200 (nM) from 9 assay(s)
EC50: min: 8, max: 158 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.31α = 90
b = 62.31β = 90
c = 158.64γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description