6CN6

RORC2 LBD complexed with compound 34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of 3-Cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist.

Schnute, M.E.Wennerstal, M.Alley, J.Bengtsson, M.Blinn, J.R.Bolten, C.W.Braden, T.Bonn, T.Carlsson, B.Caspers, N.Chen, M.Choi, C.Collis, L.P.Crouse, K.Farnegardh, M.Fennell, K.F.Fish, S.Flick, A.C.Goos-Nilsson, A.Gullberg, H.Harris, P.K.Heasley, S.E.Hegen, M.Hromockyj, A.E.Hu, X.Husman, B.Janosik, T.Jones, P.Kaila, N.Kallin, E.Kauppi, B.Kiefer, J.R.Knafels, J.Koehler, K.Kruger, L.Kurumbail, R.G.Kyne Jr., R.E.Li, W.Lofstedt, J.Long, S.A.Menard, C.A.Mente, S.Messing, D.Meyers, M.J.Napierata, L.Noteberg, D.Nuhant, P.Pelc, M.J.Prinsen, M.J.Rhonnstad, P.Backstrom-Rydin, E.Sandberg, J.Sandstrom, M.Shah, F.Sjoberg, M.Sundell, A.Taylor, A.P.Thorarensen, A.Trujillo, J.I.Trzupek, J.D.Unwalla, R.Vajdos, F.F.Weinberg, R.A.Wood, D.C.Xing, L.Zamaratski, E.Zapf, C.W.Zhao, Y.Wilhelmsson, A.Berstein, G.

(2018) J Med Chem 61: 10415-10439

  • DOI: 10.1021/acs.jmedchem.8b00392
  • Primary Citation of Related Structures:  
    6CN6, 6CN5

  • PubMed Abstract: 
  • The nuclear hormone receptor retinoic acid receptor-related orphan C2 (RORC2, also known as RORγt) is a promising target for the treatment of autoimmune diseases. A small molecule, inverse agonist of the receptor is anticipated to reduce production of IL-17, a key proinflammatory cytokine ...

    The nuclear hormone receptor retinoic acid receptor-related orphan C2 (RORC2, also known as RORγt) is a promising target for the treatment of autoimmune diseases. A small molecule, inverse agonist of the receptor is anticipated to reduce production of IL-17, a key proinflammatory cytokine. Through a high-throughput screening approach, we identified a molecule displaying promising binding affinity for RORC2, inhibition of IL-17 production in Th17 cells, and selectivity against the related RORA and RORB receptor isoforms. Lead optimization to improve the potency and metabolic stability of this hit focused on two key design strategies, namely, iterative optimization driven by increasing lipophilic efficiency and structure-guided conformational restriction to achieve optimal ground state energetics and maximize receptor residence time. This approach successfully identified 3-cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide as a potent and selective RORC2 inverse agonist, demonstrating good metabolic stability, oral bioavailability, and the ability to reduce IL-17 levels and skin inflammation in a preclinical in vivo animal model upon oral administration.


    Organizational Affiliation

    Karo Bio AB (now Karo Pharma AB) , 111 48 Stockholm , Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA259Homo sapiensMutation(s): 2 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F7J
Query on F7J

Download Ideal Coordinates CCD File 
B [auth A]3-cyano-N-{3-[1-(cyclopentanecarbonyl)piperidin-4-yl]-1,4-dimethyl-1H-indol-5-yl}benzamide
C29 H32 N4 O2
HQKLWNNRWVVUSC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F7JIC50:  5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.84α = 90
b = 90.84β = 90
c = 138.252γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AutoPROCdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-03-07 
  • Released Date: 2018-09-05 
  • Deposition Author(s): Kauppi, B., Vajdos, F.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-01
    Changes: Data collection, Database references