5TX5 | pdb_00005tx5

Rip1 Kinase ( flag 1-294, C34A, C127A, C233A, C240A) with GSK772


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 
    0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of a First-in-Class Receptor Interacting Protein 1 (RIP1) Kinase Specific Clinical Candidate (GSK2982772) for the Treatment of Inflammatory Diseases.

Harris, P.A.Berger, S.B.Jeong, J.U.Nagilla, R.Bandyopadhyay, D.Campobasso, N.Capriotti, C.A.Cox, J.A.Dare, L.Dong, X.Eidam, P.M.Finger, J.N.Hoffman, S.J.Kang, J.Kasparcova, V.King, B.W.Lehr, R.Lan, Y.Leister, L.K.Lich, J.D.MacDonald, T.T.Miller, N.A.Ouellette, M.T.Pao, C.S.Rahman, A.Reilly, M.A.Rendina, A.R.Rivera, E.J.Schaeffer, M.C.Sehon, C.A.Singhaus, R.R.Sun, H.H.Swift, B.A.Totoritis, R.D.Vossenkamper, A.Ward, P.Wisnoski, D.D.Zhang, D.Marquis, R.W.Gough, P.J.Bertin, J.

(2017) J Med Chem 60: 1247-1261

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01751
  • Primary Citation Related Structures: 
    5TX5

  • PubMed Abstract: 

    RIP1 regulates necroptosis and inflammation and may play an important role in contributing to a variety of human pathologies, including immune-mediated inflammatory diseases. Small-molecule inhibitors of RIP1 kinase that are suitable for advancement into the clinic have yet to be described. Herein, we report our lead optimization of a benzoxazepinone hit from a DNA-encoded library and the discovery and profile of clinical candidate GSK2982772 (compound 5), currently in phase 2a clinical studies for psoriasis, rheumatoid arthritis, and ulcerative colitis. Compound 5 potently binds to RIP1 with exquisite kinase specificity and has excellent activity in blocking many TNF-dependent cellular responses. Highlighting its potential as a novel anti-inflammatory agent, the inhibitor was also able to reduce spontaneous production of cytokines from human ulcerative colitis explants. The highly favorable physicochemical and ADMET properties of 5, combined with high potency, led to a predicted low oral dose in humans.


  • Organizational Affiliation
    • Centre for Immunobiology, Blizard Institute, Barts, and The London School of Medicine and Dentistry, Queen Mary University of London , E1 2AD London, U.K.

Macromolecule Content 

  • Total Structure Weight: 69.95 kDa 
  • Atom Count: 4,220 
  • Modeled Residue Count: 522 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
303Homo sapiensMutation(s): 4 
Gene Names: RIPK1RIPRIP1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
PHAROS:  Q13546
GTEx:  ENSG00000137275 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13546
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7MJ

Query on 7MJ



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
3-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1H-1,2,4-triazole-5-carboxamide
C20 H19 N5 O3
LYPAFUINURXJSG-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.774α = 90
b = 101.246β = 90
c = 129.753γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Advisory, Data collection, Database references