6RNA | pdb_00006rna

RIP2 Kinase Catalytic Domain complex with 2({4[(1,3benzothiazol5yl)amino]6(2methylpropane2sulfonyl)quinazolin7yl}oxy)ethan1ol

• PDB DOI: https://doi.org/10.2210/pdb6RNA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-05-08 Released: 2019-07-17 
• Deposition Author(s): Convery, M.A., Haile, P.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Discovery of a First-in-Class Receptor Interacting Protein 2 (RIP2) Kinase Specific Clinical Candidate, 2-((4-(Benzo[d]thiazol-5-ylamino)-6-(tert-butylsulfonyl)quinazolin-7-yl)oxy)ethyl Dihydrogen Phosphate, for the Treatment of Inflammatory Diseases.

Haile, P.A., Casillas, L.N., Votta, B.J., Wang, G.Z., Charnley, A.K., Dong, X., Bury, M.J., Romano, J.J., Mehlmann, J.F., King, B.W., Erhard, K.F., Hanning, C.R., Lipshutz, D.B., Desai, B.M., Capriotti, C.A., Schaeffer, M.C., Berger, S.B., Mahajan, M.K., Reilly, M.A., Nagilla, R., Rivera, E.J., Sun, H.H., Kenna, J.K., Beal, A.M., Ouellette, M.T., Kelly, M., Stemp, G., Convery, M.A., Vossenkamper, A., MacDonald, T.T., Gough, P.J., Bertin, J., Marquis, R.W.

(2019) J Med Chem 62: 6482-6494

• PubMed: 31265286 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00575
• Primary Citation Related Structures: 
  6RN8, 6RNA


• PubMed Abstract: 
  

  RIP2 kinase has been identified as a key signal transduction partner in the NOD2 pathway contributing to a variety of human pathologies, including immune-mediated inflammatory diseases. Small-molecule inhibitors of RIP2 kinase or its signaling partners on the NOD2 pathway that are suitable for advancement into the clinic have yet to be described. Herein, we report our discovery and profile of the prodrug clinical compound, inhibitor 3 , currently in phase 1 clinical studies. Compound 3 potently binds to RIP2 kinase with good kinase specificity and has excellent activity in blocking many proinflammatory cytokine responses in vivo and in human IBD explant samples. The highly favorable physicochemical and ADMET properties of 3 combined with high potency led to a predicted low oral dose in humans.

---

Organizational Affiliation: 
• GlaxoSmithKline , Collegeville Road , Collegeville , Pennsylvania 19426 , United States.
GlaxoSmithKline , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.
Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry , Queen Mary University of London , London E1 2AD , U.K.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.28 kDa 
• Atom Count: 4,828 
• Modeled Residue Count: 561 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 2	A, B	311	Homo sapiens	Mutation(s): 0  Gene Names: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens) Explore O43353  Go to UniProtKB:  O43353
PHAROS:  O43353 GTEx:  ENSG00000104312

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KA2 (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-[4-(1,3-benzothiazol-5-ylamino)-6-~{tert}-butylsulfonyl-quinazolin-7-yl]oxyethanol C21 H22 N4 O4 S2 UHDOJINBFLDQJM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KA2	BindingDB:  6RNA	IC50: min: 2, max: 92 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.42	α = 90
b = 132.42	β = 90
c = 107.17	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Convery, M.A., Haile, P.A.

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description