3PRE

Quinazolines with intra-molecular hydrogen bonding scaffold (iMHBS) as PI3K/mTOR dual inhibitors.

• PDB DOI: https://doi.org/10.2210/pdb3PRE/pdb

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


• Deposited: 2010-11-29 Released: 2011-02-09 
• Deposition Author(s): Knighton, D.R., Greasley, S.E., Rodgers, C.M.-L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.295 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 

Literature

Quinazolines with intra-molecular hydrogen bonding scaffold (iMHBS) as PI3K/mTOR dual inhibitors.

Liu, K.K., Huang, X., Bagrodia, S., Chen, J.H., Greasley, S., Cheng, H., Sun, S., Knighton, D., Rodgers, C., Rafidi, K., Zou, A., Xiao, J., Yan, S.

(2011) Bioorg Med Chem Lett 21: 1270-1274

• PubMed: 21269826 
• DOI: https://doi.org/10.1016/j.bmcl.2010.12.026
• Primary Citation of Related Structures:  
  3PRE, 3PRZ, 3PS6


• PubMed Abstract: 
  

  Intra-molecular hydrogen bonding was introduced to the quinazoline motif to form a pseudo ring (intra-molecular H-bond scaffold, iMHBS) to mimic our previous published core structures, pyrido[2.3-D]pyrimidin-7-one and pteridinone, as PI3K/mTOR dual inhibitors. This design results in potent PI3K/mTOR dual inhibitors and the purposed intra-molecular hydrogen bonding structure is well supported by co-crystal structure in PI3Kγ enzyme. In addition, a novel synthetic route was developed for these analogs.

---

Organizational Affiliation: 

Pfizer Global Research and Development, Chemistry Department, 10770 Science Center Drive, La Jolla, CA 92120, USA. [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: 111.08 kDa 
• Atom Count: 6,813 
• Modelled Residue Count: 839 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3RE	B [auth A]	2-amino-8-(trans-4-methoxycyclohexyl)-4-methyl-6-(1H-pyrazol-3-yl)pyrido[2,3-d]pyrimidin-7(8H)-one C18 H22 N6 O2 UDXSDTPXGCELRI-HAQNSBGRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.295 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.541	α = 90
b = 67.276	β = 95.77
c = 106.529	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Knighton, D.R., Greasley, S.E., Rodgers, C.M.-L.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations