4L23

Crystal Structure of p110alpha complexed with niSH2 of p85alpha and PI-103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of PI3K alpha Complexed with PI103 and Its Derivatives: New Directions for Inhibitors Design.

Zhao, Y.Zhang, X.Chen, Y.Lu, S.Peng, Y.Wang, X.Guo, C.Zhou, A.Zhang, J.Luo, Y.Shen, Q.Ding, J.Meng, L.Zhang, J.

(2014) ACS Med Chem Lett 5: 138-142

  • DOI: 10.1021/ml400378e
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The phosphatidylinositol 3-kinase (PI3K) signaling pathway plays important roles in cell proliferation, growth, and survival. Hyperactivated PI3K is frequently found in a wide variety of human cancers, validating it as a promising target for cancer t ...

    The phosphatidylinositol 3-kinase (PI3K) signaling pathway plays important roles in cell proliferation, growth, and survival. Hyperactivated PI3K is frequently found in a wide variety of human cancers, validating it as a promising target for cancer therapy. We determined the crystal structure of the human PI3Kα-PI103 complex to unravel molecular interactions. Based on the structure, substitution at the R1 position of the phenol portion of PI103 was demonstrated to improve binding affinity via forming a new H-bond with Lys802 at the bottom of the ATP catalytic site. Interestingly, the crystal structure of the PI3Kα-9d complex revealed that the flexibility of Lys802 can also induce additional space at the catalytic site for further modification. Thus, these crystal structures provide a molecular basis for the strong and specific interactions and demonstrate the important role of Lys802 in the design of novel PI3Kα inhibitors.


    Organizational Affiliation

    Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine , Shanghai 200025, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformA1068Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
NIH Common Fund Data Resources
PHAROS  P42336
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alphaB324Homo sapiensMutation(s): 0 
Gene Names: GRB1PIK3R1
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS  P27986
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X6K
Query on X6K

Download CCD File 
A
3-(4-MORPHOLIN-4-YLPYRIDO[3',2':4,5]FURO[3,2-D]PYRIMIDIN-2-YL)PHENOL
C19 H16 N4 O3
TUVCWJQQGGETHL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X6KIC50:  8   nM  BindingDB
X6KIC50:  4.5   nM  BindingDB
X6KIC50:  75   nM  BindingDB
X6KIC50:  11   nM  BindingDB
X6KKd:  3.200000047683716   nM  BindingDB
X6KIC50:  8   nM  BindingDB
X6KIC50:  150   nM  BindingDB
X6KIC50:  7.5   nM  BindingDB
X6KIC50:  3.5999999046325684   nM  BindingDB
X6KKd:  1.399999976158142   nM  BindingDB
X6KIC50:  2   nM  BindingDB
X6KIC50:  6.099999904632568   nM  BindingDB
X6KIC50:  17   nM  BindingDB
X6KIC50:  18   nM  BindingDB
X6KKd:  3   nM  BindingDB
X6KIC50:  8.699999809265137   nM  BindingDB
X6KIC50:  4.400000095367432   nM  BindingDB
X6KIC50:  6.800000190734863   nM  BindingDB
X6KIC50:  1.7999999523162842   nM  BindingDB
X6KIC50:  40   nM  BindingDB
X6KIC50:  5.800000190734863   nM  BindingDB
X6KIC50:  2   nM  BindingDB
X6KKd:  1.5   nM  BindingDB
X6KKd:  1.2999999523162842   nM  BindingDB
X6KKd:  2.9000000953674316   nM  BindingDB
X6KKd:  3.4000000953674316   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.628α = 90
b = 136.377β = 90
c = 151.487γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description