Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 164306.66 
• Atom Count: 10100 
• Residue Count: 1396 
• Unique protein chains: 2

4WAF

Crystal Structure of a novel tetrahydropyrazolo[1,5-a]pyrazine in an engineered PI3K alpha

• DOI: 10.2210/pdb4WAF/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): 5 


• Deposited: 2014-08-29 Released: 2014-12-31 
• Deposition Author(s): Knapp, M.S., Elling, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 

Literature

Structure-Based Drug Design of Novel Potent and Selective Tetrahydropyrazolo[1,5-a]pyrazines as ATR Inhibitors.

Barsanti, P.A., Aversa, R.J., Jin, X., Pan, Y., Lu, Y., Elling, R., Jain, R., Knapp, M., Lan, J., Lin, X., Rudewicz, P., Sim, J., Taricani, L., Thomas, G., Xiao, L., Yue, Q.

(2015) Acs Med.Chem.Lett. 6: 37-41

• PubMed: 25589927 
• DOI: 10.1021/ml500353p


• PubMed Abstract: 
  

A saturation strategy focused on improving the selectivity and physicochemical properties of ATR inhibitor HTS hit 1 led to a novel series of highly potent and selective tetrahydropyrazolo[1,5-a]pyrazines. Use of PI3Kα mutants as ATR crystal structure surrogates was instrumental in providing cocrystal structures to guide the medicinal chemistry designs. Detailed DMPK studies involving cyanide and GSH as trapping agents during microsomal incubations, in addition to deuterium-labeled compounds as mechanistic probes uncovered the molecular basis for the observed CYP3A4 TDI in the series.

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Organizational Affiliation: 

Global Discovery Chemistry Oncology, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	1073	Homo sapiens	Mutation(s): 4  Gene Names: PIK3CA EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens) Go to Gene View: PIK3CA Go to UniProtKB:  P42336

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	323	Homo sapiens	Mutation(s): 1  Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens) Go to Gene View: PIK3R1 Go to UniProtKB:  P27986

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3K6	A	N,N-dimethyl-4-[(6R)-6-methyl-5-(1H-pyrrolo[2,3-b]pyridin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-3-yl]benzenesulfonamide C22 H24 N6 O2 S UGAYOLUDSWRLMK-OAHLLOKOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3K6	IC50: >10000 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.247 
• R-Value Work: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 104.483	α = 90.00
b = 106.525	β = 90.00
c = 133.507	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-29 
• Released Date: 2014-12-31 
• Deposition Author(s): Knapp, M.S., Elling, R.A.

Revision History 

• Version 1.0: 2014-12-31
  Type: Initial release
• Version 1.1: 2015-01-28
  Type: Database references