5UBR

CRYSTAL STRUCTURE OF PI3K ALPHA IN COMPLEX WITH A 7-(3-(PIPERAZIN-1-YL)PHENYL)PYRROLO[2,1-F][1,2,4] TRIAZIN-4-AMINE DERIVIATINE

• PDB DOI: https://doi.org/10.2210/pdb5UBR/pdb

• Classification: TRANSFERASE/TRANSFERASE REGULATOR
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2016-12-21 Released: 2017-02-08 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Discovery of 7-(3-(piperazin-1-yl)phenyl)pyrrolo[2,1-f][1,2,4]triazin-4-amine derivatives as highly potent and selective PI3K delta inhibitors.

Qin, L.Y., Ruan, Z., Cherney, R.J., Dhar, T.G., Neels, J., Weigelt, C.A., Sack, J.S., Srivastava, A.S., Cornelius, L.A., Tino, J.A., Stefanski, K., Gu, X., Xie, J., Susulic, V., Yang, X., Yarde-Chinn, M., Skala, S., Bosnius, R., Goldstein, C., Davies, P., Ruepp, S., Salter-Cid, L., Bhide, R.S., Poss, M.A.

(2017) Bioorg Med Chem Lett 27: 855-861

• PubMed: 28108251 
• DOI: https://doi.org/10.1016/j.bmcl.2017.01.016
• Primary Citation of Related Structures:  
  5UBR, 5UBT


• PubMed Abstract: 
  

  As demonstrated in preclinical animal models, the disruption of PI3Kδ expression or its activity leads to a decrease in inflammatory and immune responses. Therefore, inhibition of PI3Kδ may provide an alternative treatment for autoimmune diseases, such as RA, SLE, and respiratory ailments. Herein, we disclose the identification of 7-(3-(piperazin-1-yl)phenyl)pyrrolo[2,1-f][1,2,4]triazin-4-amine derivatives as highly potent, selective and orally bioavailable PI3Kδ inhibitors. The lead compound demonstrated efficacy in an in vivo mouse KLH model.

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Organizational Affiliation: 

Bristol-Myers Squibb, Rt. 206 & Province Line Road, Princeton, NJ 08540, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 110.28 kDa 
• Atom Count: 7,136 
• Modelled Residue Count: 887 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	944	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
85S	B [auth A]	1-[4-(3-{4-amino-5-[1-(oxan-4-yl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)piperazin-1-yl]ethan-1-one C26 H30 N8 O2 BYWWTRGEAVDHNY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.645	α = 90
b = 134.805	β = 90
c = 142.342	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-02-22
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references