3ZIM

Discovery of a potent and isoform-selective targeted covalent inhibitor of the lipid kinase PI3Kalpha

Structural Biology Knowledgebase: 3ZIM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZIM

Classification: TRANSFERASE

Total Structure Weight: 109980.99

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM A 940 Homo sapiens EC#: 2.7.1.153 IUBMB
Fragment: N-TERMINAL TRUNCATED, RESIDUES 107-1046
Details: LIGAND COVALENTLY LINKED TO CYS862
Gene Name(s): PIK3CA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KKR
Query on KKR

A 1-[4-[[2-(1H-indazol-4-yl)-4-morpholin-4- yl-thieno[3,2-d]pyrimidin-6-yl]methyl]piperazin- 1-yl]-6-methyl-hept-5-ene-1,4-dione
4-dione, (Synonym)
C30 H35 N7 O3 S
DLNUPKDFXMWRFP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
KKR EC50: 10 nM (100) BindingDB
IC50: 6.8 nM (100) BindingDB

N/A in BindingMoad
IC50: 6.8 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.213
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.34 α = 90.00
b = 135.03 β = 90.00
c = 142.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-09
  • Released Date: 2013-02-13
  • Deposition author(s): Nacht, M., Qiao, L., Sheets, M.P., Martin, T.S., Labenski, M., Mazdiyasni, H., Karp, R., Zhu, Z., Chaturvedi, P., Bhavsar, D., Niu, D., Westlin, W., Petter, R.C., Medikonda, A.P., Jestel, A., Blaesse, M., Singh, J.

Revision History

  • 2013-02-27
    Type: Citation | Details: JRNL