2X38

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with IC87114.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The P110D Structure: Mechanisms for Selectivity and Potency of New Pi(3)K Inhibitors

Berndt, A.Miller, S.Williams, O.Lee, D.D.Houseman, B.T.Pacold, J.I.Gorrec, F.Hon, W.-C.Liu, Y.Rommel, C.Gaillard, P.Ruckle, T.Schwarz, M.K.Shokat, K.M.Shaw, J.P.Williams, R.L.

(2010) Nat.Chem.Biol. 6: 117

  • DOI: 10.1038/nchembio.293
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deregulation of the phosphoinositide-3-OH kinase (PI(3)K) pathway has been implicated in numerous pathologies including cancer, diabetes, thrombosis, rheumatoid arthritis and asthma. Recently, small-molecule and ATP-competitive PI(3)K inhibitors with ...

    Deregulation of the phosphoinositide-3-OH kinase (PI(3)K) pathway has been implicated in numerous pathologies including cancer, diabetes, thrombosis, rheumatoid arthritis and asthma. Recently, small-molecule and ATP-competitive PI(3)K inhibitors with a wide range of selectivities have entered clinical development. In order to understand the mechanisms underlying the isoform selectivity of these inhibitors, we developed a new expression strategy that enabled us to determine to our knowledge the first crystal structure of the catalytic subunit of the class IA PI(3)K p110 delta. Structures of this enzyme in complex with a broad panel of isoform- and pan-selective class I PI(3)K inhibitors reveal that selectivity toward p110 delta can be achieved by exploiting its conformational flexibility and the sequence diversity of active site residues that do not contact ATP. We have used these observations to rationalize and synthesize highly selective inhibitors for p110 delta with greatly improved potencies.


    Organizational Affiliation

    Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
A
940Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
Find proteins for O35904 (Mus musculus)
Go to UniProtKB:  O35904
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IC8
Query on IC8

Download SDF File 
Download CCD File 
A
2-[(6-AMINO-9H-PURIN-9-YL)METHYL]-5-METHYL-3-(2-METHYLPHENYL)QUINAZOLIN-4(3H)-ONE
C22 H19 N7 O
GNWHRHGTIBRNSM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IC8IC50: 25 - 500 nM (94) BINDINGDB
IC8Ki: 13 - 20 nM (94) BINDINGDB
IC8IC50: 130 nM BINDINGMOAD
IC8IC50: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.420α = 90.00
b = 64.660β = 103.39
c = 116.900γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
TRUNCATEdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2019-04-24
    Type: Data collection, Other, Source and taxonomy