4NEU

X-ray structure of Receptor Interacting Protein 1 (RIP1)kinase domain with a 1-aminoisoquinoline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4NEU/pdb

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


• Deposited: 2013-10-30 Released: 2013-11-20 
• Deposition Author(s): Nolte, R.T., Ward, P., kahler, K.M., Campobasso, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Discovery of Small Molecule RIP1 Kinase Inhibitors for the Treatment of Pathologies Associated with Necroptosis.

Harris, P.A., Bandyopadhyay, D., Berger, S.B., Campobasso, N., Capriotti, C.A., Cox, J.A., Dare, L., Finger, J.N., Hoffman, S.J., Kahler, K.M., Lehr, R., Lich, J.D., Nagilla, R., Nolte, R.T., Ouellette, M.T., Pao, C.S., Schaeffer, M.C., Smallwood, A., Sun, H.H., Swift, B.A., Totoritis, R.D., Ward, P., Marquis, R.W., Bertin, J., Gough, P.J.

(2013) ACS Med Chem Lett 4: 1238-1243

• PubMed: 24900635 
• DOI: https://doi.org/10.1021/ml400382p
• Primary Citation of Related Structures:  
  4NEU


• PubMed Abstract: 
  

  Potent inhibitors of RIP1 kinase from three distinct series, 1-aminoisoquinolines, pyrrolo[2,3-b]pyridines, and furo[2,3-d]pyrimidines, all of the type II class recognizing a DLG-out inactive conformation, were identified from screening of our in-house kinase focused sets. An exemplar from the furo[2,3-d]pyrimidine series showed a dose proportional response in protection from hypothermia in a mouse model of TNFα induced lethal shock.

---

Organizational Affiliation: 

Pattern Recognition Receptor DPU and Platform Technology & Science, GlaxoSmithKline , Collegeville Road, Collegeville, Pennsylvania 19426, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.25 kDa 
• Atom Count: 4,629 
• Modelled Residue Count: 554 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B	333	Homo sapiens	Mutation(s): 0  Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
PHAROS:  Q13546 GTEx:  ENSG00000137275

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q1A	D [auth A], E [auth B]	1-[4-(1-aminoisoquinolin-5-yl)phenyl]-3-(5-tert-butyl-1,2-oxazol-3-yl)urea C23 H23 N5 O2 SLRYMOUSQMDJPH-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q1A	BindingDB:  4NEU	IC50: min: 10, max: 630 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.249	α = 90
b = 149.249	β = 90
c = 187.67	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Nolte, R.T., Ward, P., kahler, K.M., Campobasso, N.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations