6NW2

Structure of human RIPK1 kinase domain in complex with compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent and selective inhibitors of receptor-interacting protein kinase 1 that lack an aromatic back pocket group.

Hamilton, G.L.Chen, H.Deshmukh, G.Eigenbrot, C.Fong, R.Johnson, A.Kohli, P.B.Lupardus, P.J.Liederer, B.M.Ramaswamy, S.Wang, H.Wang, J.Xu, Z.Zhu, Y.Vucic, D.Patel, S.

(2019) Bioorg Med Chem Lett 29: 1497-1501

  • DOI: 10.1016/j.bmcl.2019.04.014
  • Primary Citation of Related Structures:  
    6NW2

  • PubMed Abstract: 
  • Receptor-interacting protein kinase 1 (RIPK1), a key component of the cellular necroptosis pathway, has gained recognition as an important therapeutic target. Pharmacologic inhibition or genetic inactivation of RIPK1 has shown promise in animal models of disease ranging from acute ischemic conditions, chronic inflammation, and neurodegeneration ...

    Receptor-interacting protein kinase 1 (RIPK1), a key component of the cellular necroptosis pathway, has gained recognition as an important therapeutic target. Pharmacologic inhibition or genetic inactivation of RIPK1 has shown promise in animal models of disease ranging from acute ischemic conditions, chronic inflammation, and neurodegeneration. We present here a class of RIPK1 inhibitors that is distinguished by a lack of a lipophilic aromatic group present in most literature inhibitors that typically occupies a hydrophobic back pocket of the protein active site. Despite not having this ubiquitous feature of many known RIPK1 inhibitors, we were able to obtain compounds with good potency, kinase selectivity, and pharmacokinetic properties in rats. The use of the lipophilic yet metabolically stable pentafluoroethyl group was critical to balancing the potency and properties of optimized analogs.


    Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: patel.snahel@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1 AB310Homo sapiensMutation(s): 0 
Gene Names: RIPK1RIPRIP1
EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
NIH Common Fund Data Resources
PHAROS:  Q13546
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L4Y
Query on L4Y

Download Ideal Coordinates CCD File 
A, B
(5R)-5-methyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide
C19 H22 N4 O3
LOTYATKNTZKNHI-RISCZKNCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L4YKi:  16   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.862α = 90
b = 96.644β = 90
c = 125.285γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references