5AR5

RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5AR2, 5AR3, 5AR4, 5AR5, 5AR7, 5AR8

  • 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 attractive target to probe the role of these pathways in disease ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2A, B326Homo sapiensMutation(s): 0 
Gene Names: RIPK2CARDIAKRICKRIP2UNQ277/PRO314/PRO34092
EC: 2.7.10.2 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens)
Explore O43353 
Go to UniProtKB:  O43353
PHAROS:  O43353
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IQ7 (Subject of Investigation/LOI)
Query on IQ7

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]2-(2-(4-CHLOROPHENYL)-1H-IMIDAZOL-5-YL)-N,1-BIS(2-METHOXYETHYL)-1H-BENZO[D]IMIDAZOLE-5-CARBOXAMIDE
C23 H24 Cl N5 O3
GALXSGLZQVWBNV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IQ7 BindingDB:  5AR5 IC50: min: 12, max: 500 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.176α = 90
b = 132.176β = 90
c = 107.667γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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