Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 108346.29 
• Atom Count: 6777 
• Residue Count: 940 
• Unique protein chains: 1

2WXK

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with INK666.

• DOI: 10.2210/pdb2WXK/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda


• Deposited: 2009-11-09 Released: 2010-01-12 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.213 

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

• PubMed: 20081827 
• DOI: 10.1038/nchembio.293
• Primary Citation of Related Structures:  
  2X38, 2WXR, 2WXQ, 2WXP, 2WXO, 2WXN, 2WXM, 2WXL, 2WXJ, 2WXI, 2WXH, 2WXG, 2WXF


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM	A	940	Mus musculus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
RW4	A	3-(2-amino-1,3-benzothiazol-6-yl)-1-{[2-(4-methylpiperazin-1-yl)quinolin-3-yl]methyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine C27 H26 N10 S UNSGOTITAWKECZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RW4	IC50: 0.5 nM (94) BINDINGDB
RW4	IC50: 0.5 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.213 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 64.362	α = 90.00
b = 143.669	β = 90.00
c = 223.121	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-09 
• Released Date: 2010-01-12 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2010-01-12
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-04-24
  Type: Data collection, Other, Source and taxonomy