7KQJ | pdb_00007kqj

CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(244-487)-L6-SRC1(678-692) IN COMPLEX WITH A NOVEL TRICYCLIC-CARBOCYLIC RORGT INVERSE AGONIST


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.254 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z8GClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Tricyclic-Carbocyclic ROR gamma t Inverse Agonists-Discovery of BMS-986313.

Yang, M.G.Beaudoin-Bertrand, M.Xiao, Z.Marcoux, D.Weigelt, C.A.Yip, S.Wu, D.R.Ruzanov, M.Sack, J.S.Wang, J.Yarde, M.Li, S.Shuster, D.J.Xie, J.H.Sherry, T.Obermeier, M.T.Fura, A.Stefanski, K.Cornelius, G.Khandelwal, P.Karmakar, A.Basha, M.Babu, V.Gupta, A.K.Mathur, A.Salter-Cid, L.Denton, R.Zhao, Q.Dhar, T.G.M.

(2021) J Med Chem 64: 2714-2724

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01992
  • Primary Citation of Related Structures:  
    7KQJ

  • PubMed Abstract: 

    SAR efforts directed at identifying RORγt inverse agonists structurally different from our clinical compound 1 (BMS-986251) led to tricyclic-carbocyclic analogues represented by 3 - 7 and culminated in the identification of 3d (BMS-986313), with structural differences distinct from 1 . The X-ray co-crystal structure of 3d with the ligand binding domain of RORγt revealed several key interactions, which are different from 1 . The in vitro and in vivo PK profiles of 3d are described. In addition, we demonstrate robust efficacy of 3d in two preclinical models of psoriasis-the IMQ-induced skin lesion model and the IL-23-induced acanthosis model. The efficacy seen with 3d in these models is comparable to the results observed with 1 .


  • Organizational Affiliation

    Research and Early Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma285Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z8G (Subject of Investigation/LOI)
Query on Z8G

Download Ideal Coordinates CCD File 
B [auth A]N-[(3R,3aS,9bS)-9b-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,2,3,3,3-heptafluoropropan-2-yl)-2,3,3a,4,5,9b-hexahydro-1H-cyclopenta[a]naphthalen-3-yl]-2-hydroxy-2-methylpropanamide
C26 H25 F8 N O4 S
JZUVTKBHDNIOHD-MIZPHKNDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z8G BindingDB:  7KQJ IC50: 6 (nM) from 1 assay(s)
EC50: min: 2.7, max: 50 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.254 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.809α = 90
b = 63.809β = 90
c = 159.923γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z8GClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2021-02-24 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description