8FAV

HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 5 ANDINDAZOLE ACID BOUND IN H12-POCKET

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Literature

Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists.

Schnute, M.E., Trujillo, J.I., Lee, K.L., Unwalla, R., Vajdos, F.F., Kauppi, B., Nuhant, P., Flick, A.C., Crouse, K.K., Zhao, Y., Samuel, A., Lombardo, V., Taylor, A.P., Brault, A.L., Knafels, J.D., Vazquez, M.L., Berstein, G.

(2023) ACS Med Chem Lett 14: 191-198

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00500
  • Primary Citation of Related Structures:  
    8FAV, 8FB1, 8FB2

  • PubMed Abstract: 

    Macrocyclic retinoic acid receptor-related orphan receptor C2 (RORC2) inverse agonists have been designed with favorable properties for topical administration. Inspired by the unanticipated bound conformation of an acyclic sulfonamide-based RORC2 ligand from cocrystal structure analysis, macrocyclic linker connections between the halves of the molecule were explored. Further optimization of analogues was accomplished to maximize potency and refine physiochemical properties (MW, lipophilicity) best suited for topical application. Compound 14 demonstrated potent inhibition of interleukin-17A (IL-17A) production by human Th17 cells and in vitro permeation through healthy human skin achieving high total compound concentration in both skin epidermis and dermis layers.

    • Organizational Affiliation: 

    Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
262Homo sapiensMutation(s): 2 
Gene Names: RORC, NR1F3, RORG, RZRG
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4Y5
Query on 4Y5
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-3-fluorobenzoic acid
C22 H10 Cl F5 N2 O3
PFVOSXMQCIFOSO-UHFFFAOYSA-N
LKY (Subject of Investigation/LOI)
Query on LKY
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		3-cyano-N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)benzamide
C27 H31 F N4 O2
AQGBWBMWWNRWNU-SFHVURJKSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.088α = 90
b = 96.922β = 91.26
c = 56.914γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-01 
    • Deposition Author(s): Vajdos, F.F.
Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary