4H3I Hydrolase Hydrolase Inhibitor date Sep 13, 2012
title Structure Of Bace Bound To 3-(5-((7ar)-2-Imino-6-(3-Methoxyp Yl)-3-Methyl-4-Oxooctahydro-1h-Pyrrolo[3,4-D]Pyrimidin-7a-Y Thiophen-3-Yl)Benzonitrile
authors C.Strickland, M.Mandal
compound source
Molecule: Beta-Secretase 1
Chain: A, B
Fragment: Unp Residues 41-454
Synonym: Aspartyl Protease 2, Asp2, Asp 2, Beta-Site Amyloi Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Memapsin-2, Membrane-Associated Aspartic Protease 2;
Ec: 3.4.23.46
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace, Bace1, Kiaa1149
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.318 89.707 131.243 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.96 Å
ligand 10V, TLA BindingDB enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDesign and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation., Mandal M, Zhu Z, Cumming JN, Liu X, Strickland C, Mazzola RD, Caldwell JP, Leach P, Grzelak M, Hyde L, Zhang Q, Terracina G, Zhang L, Chen X, Kuvelkar R, Kennedy ME, Favreau L, Cox K, Orth P, Buevich A, Voigt J, Wang H, Kazakevich I, McKittrick BA, Greenlee W, Parker EM, Stamford AW, J Med Chem. 2012 Oct 1. PMID:22989333
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (4h3i.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (4h3i.pdb2.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 4H3I
  • CSU: Contacts of Structural Units for 4H3I
  • Structure Factors (1297 Kb)
  • Retrieve 4H3I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4H3I from S2C, [Save to disk]
  • Re-refined 4h3i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4H3I 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 4H3I
  • 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
  • 3D motif for 4H3I, from MSDmotif at EBI
  • Fold representative 4h3i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4h3i_A] [4h3i_B] [4h3i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4H3I
  • Community annotation for 4H3I at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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