5AR7

RIP2 Kinase Catalytic Domain (1 - 310) complex with Biaryl Urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of Human Rip2 Kinase Catalytic Domain Complexed with ATP-Competitive Inhibitors: Foundations for Understanding Inhibitor Selectivity.

Charnley, A.K.Convery, M.A.Lakdawala Shah, A.Jones, E.Hardwicke, P.Bridges, A.Ouellette, M.Totoritis, R.Schwartz, B.King, B.W.Wisnoski, D.D.Kang, J.Eidam, P.M.Votta, B.J.Gough, P.J.Marquis, R.W.Bertin, J.Casillas, L.

(2015) Bioorg.Med.Chem. 23: 7000

  • DOI: 10.1016/j.bmc.2015.09.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Receptor interacting protein 2 (RIP2) is an intracellular kinase and key signaling partner for the pattern recognition receptors NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins 1 and 2). As such, RIP2 represents an attrac ...

    Receptor interacting protein 2 (RIP2) is an intracellular kinase and key signaling partner for the pattern recognition receptors NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins 1 and 2). As such, RIP2 represents an attractive target to probe the role of these pathways in disease. In an effort to design potent and selective inhibitors of RIP2 we established a crystallographic system and determined the structure of the RIP2 kinase domain in an apo form and also in complex with multiple inhibitors including AMP-PCP (β,γ-Methyleneadenosine 5'-triphosphate, a non-hydrolysable adenosine triphosphate mimic) and structurally diverse ATP competitive chemotypes identified via a high-throughput screening campaign. These structures represent the first set of diverse RIP2-inhibitor co-crystal structures and demonstrate that the protein possesses the ability to adopt multiple DFG-in as well as DFG-out and C-helix out conformations. These structures reveal key protein-inhibitor structural insights and serve as the foundation for establishing a robust structure-based drug design effort to identify both potent and highly selective inhibitors of RIP2 kinase.


    Organizational Affiliation

    Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapy Area, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426, USA. Electronic address: adam.k.charnley@gsk.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
A, B
326Homo sapiensMutation(s): 0 
Gene Names: RIPK2 (CARDIAK, RICK, RIP2)
EC: 2.7.11.1
Find proteins for O43353 (Homo sapiens)
Go to Gene View: RIPK2
Go to UniProtKB:  O43353
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR8
Query on SR8

Download SDF File 
Download CCD File 
A, B
1-(5-TERT-BUTYL-1,2-OXAZOL-3-YL)-3-(4-PYRIDIN-4-YLOXYPHENYL)UREA
C19 H20 N4 O3
XKNAGLMNQADBQE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SR8IC50: 63 - 320 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.600α = 90.00
b = 131.600β = 90.00
c = 107.540γ = 120.00
Software Package:
Software NamePurpose
REFMACphasing
SCALAdata scaling
MOSFLMdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references