5DXU Transferase Inhibitor date Sep 23, 2015
title P110deltap85alpha With Gdc-0326
authors T.P.Heffron, R.A.Heald, C.Ndubaku, B.Q.Wei, M.Augustin, S.Do, K.Ed C.Eigenbrot, L.Friedman, E.Gancia, P.S.Jackson, G.Jones, A.Koles L.B.Lee, J.D.Lesnick, C.Lewis, N.Mclean, M.Mortle, J.Nonomiya, J. S.Price, W.W.Prior, L.Salphati, S.Sideris, S.T.Staben, S.Steinba V.Tsui, J.Wallin, D.Sampath, A.Olivero
compound source
Molecule: Phosphatidylinositol 4,5-Bisphosphate 3-Kinase Ca Subunit Delta Isoform;
Chain: A
Synonym: Ptdins-3-Kinase Subunit Delta,Phosphatidylinositol Bisphosphate 3-Kinase 110 Kda Catalytic Subunit Delta,P110d
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pik3cd
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Phosphatidylinositol 3-Kinase Regulatory Subunit
Chain: B
Fragment: Unp Residues 431-599
Synonym: Ptdins-3-Kinase Regulatory Subunit Alpha, Phosphatidylinositol 3-Kinase 85 Kda Regulatory Subunit Alp 3-Kinase Regulatory Subunit P85-Alpha;
Engineered: Yes

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Gene: Pik3r1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.248 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
91.049 108.749 142.427 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.64 Å
ligand 5H5 enzyme Transferase E.C. BRENDA

Primary referenceThe Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1 ,4]oxazepin-9-yl)oxy)propanamide (GDC-0326)., Heffron TP, Heald RA, Ndubaku C, Wei B, Augistin M, Do S, Edgar K, Eigenbrot C, Friedman L, Gancia E, Jackson PS, Jones G, Kolesnikov A, Lee LB, Lesnick JD, Lewis C, McLean N, Mortl M, Nonomiya J, Pang J, Price S, Prior WW, Salphati L, Sideris S, Staben ST, Steinbacher S, Tsui V, Wallin J, Sampath D, Olivero AG, J Med Chem. 2016 Jan 20. PMID:26741947
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (387 Kb) [Save to disk]
  • Biological Unit Coordinates (5dxu.pdb1.gz) 380 Kb
  • LPC: Ligand-Protein Contacts for 5DXU
  • CSU: Contacts of Structural Units for 5DXU
  • Structure Factors (350 Kb)
  • Retrieve 5DXU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DXU from S2C, [Save to disk]
  • Re-refined 5dxu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DXU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5DXU
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5dxu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dxu] [5dxu_B] [5dxu_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DXU: [PI3K_C2] [PI3K_p85B] [PI3K_rbd] [PI3Ka] [PI3Kc ] by SMART
  • Other resources with information on 5DXU
  • Community annotation for 5DXU at PDBWiki (http://pdbwiki.org)

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