5HX6

Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

DNA-Encoded Library Screening Identifies Benzo[b][1,4]oxazepin-4-ones as Highly Potent and Monoselective Receptor Interacting Protein 1 Kinase Inhibitors.

Harris, P.A., King, B.W., Bandyopadhyay, D., Berger, S.B., Campobasso, N., Capriotti, C.A., Cox, J.A., Dare, L., Dong, X., Finger, J.N., Grady, L.C., Hoffman, S.J., Jeong, J.U., Kang, J., Kasparcova, V., Lakdawala, A.S., Lehr, R., McNulty, D.E., Nagilla, R., Ouellette, M.T., Pao, C.S., Rendina, A.R., Schaeffer, M.C., Summerfield, J.D., Swift, B.A., Totoritis, R.D., Ward, P., Zhang, A., Zhang, D., Marquis, R.W., Bertin, J., Gough, P.J.

(2016) J Med Chem 59: 2163-2178

  • DOI: 10.1021/acs.jmedchem.5b01898
  • Primary Citation of Related Structures:  
    5HX6

  • PubMed Abstract: 

    • The recent discovery of the role of receptor interacting protein 1 (RIP1) kinase in tumor necrosis factor (TNF)-mediated inflammation has led to its emergence as a highly promising target for the treatment of multiple inflammatory diseases. We screened RIP1 against GSK's DNA-encoded small-molecule libraries and identified a novel highly potent benzoxazepinone inhibitor series ...

    The recent discovery of the role of receptor interacting protein 1 (RIP1) kinase in tumor necrosis factor (TNF)-mediated inflammation has led to its emergence as a highly promising target for the treatment of multiple inflammatory diseases. We screened RIP1 against GSK's DNA-encoded small-molecule libraries and identified a novel highly potent benzoxazepinone inhibitor series. We demonstrate that this template possesses complete monokinase selectivity for RIP1 plus unique species selectivity for primate versus nonprimate RIP1. We elucidate the conformation of RIP1 bound to this benzoxazepinone inhibitor driving its high kinase selectivity and design specific mutations in murine RIP1 to restore potency to levels similar to primate RIP1. This series differentiates itself from known RIP1 inhibitors in combining high potency and kinase selectivity with good pharmacokinetic profiles in rodents. The favorable developability profile of this benzoxazepinone template, as exemplified by compound 14 (GSK'481), makes it an excellent starting point for further optimization into a RIP1 clinical candidate.

    Organizational Affiliation: 

    Platform Technology & Science, GlaxoSmithKline , King of Prussia, Pennsylvania 19406, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1A, B303Homo sapiensMutation(s): 4 
Gene Names: RIPK1, RIP, RIP1
EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
NIH Common Fund Data Resources
PHAROS:  Q13546
GTEx:  ENSG00000137275
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
65U
Query on 65U
Download Ideal Coordinates CCD File 
 C [auth A], D [auth B]5-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1,2-oxazole-3-carboxamide
C21 H19 N3 O4
KNOUWGGQMADIBV-KRWDZBQOSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
65UKi:  0.800000011920929   nM  BindingDB
65UIC50:  1.600000023841858   nM  BindingDB
65UIC50:  2.799999952316284   nM  BindingDB
65UIC50:  10   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.6α = 90
b = 101.35β = 90
c = 131.06γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references