5T8F Transferase Transferase Inhibitor date Sep 07, 2016
title P110deltap85alpha With Taselisib (Gdc-0032)
authors M.Moertl, S.Steinbacher, C.Eigenbrot
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: Pi3-Kinase P110 Delta And P85 Fragment
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 0.242 R_Free 0.304
length a length b length c angle alpha angle beta angle gamma
91.096 108.604 142.223 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.91 Å
ligand 799 enzyme Transferase E.C. BRENDA

Primary referenceStructure-Based Design of Tricyclic NF-kappaB Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K)., Castanedo GM, Blaquiere N, Beresini M, Bravo B, Brightbill H, Chen J, Cui HF, Eigenbrot C, Everett C, Feng J, Godemann R, Gogol E, Hymowitz S, Johnson A, Kayagaki N, Kohli PB, Knuppel K, Kraemer J, Kruger S, Loke P, McEwan P, Montalbetti C, Roberts DA, Smith M, Steinbacher S, Sujatha-Bhaskar S, Takahashi R, Wang X, Wu LC, Zhang Y, Staben ST, J Med Chem. 2017 Jan 12. doi: 10.1021/acs.jmedchem.6b01363. PMID:28005357
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (370 Kb) [Save to disk]
  • Biological Unit Coordinates (5t8f.pdb1.gz) 362 Kb
  • LPC: Ligand-Protein Contacts for 5T8F
  • CSU: Contacts of Structural Units for 5T8F
  • Structure Factors (274 Kb)
  • Retrieve 5T8F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5T8F from S2C, [Save to disk]
  • Re-refined 5t8f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5T8F 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 5T8F
  • 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 5t8f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5t8f_A] [5t8f] [5t8f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5T8F
  • Community annotation for 5T8F at PDBWiki (http://pdbwiki.org)

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