5YGY Hydrolase Inhibitor date Sep 27, 2017
title Crystal Structure Of Bace1 In Complex With (S)-N-(3-(2-Amino (Fluoromethyl)-4 -Methyl-4h-1,3-Oxazin-4-Yl)-4-Fluorophenyl Cyanopicolinamide
authors K.Fuchino, Y.Mitsuoka, M.Masui, N.Kurose, S.Yoshida, K.Komano, T.Y M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnis Y.Kido, T.Fukushima, H.Miyajima, S.Hiroyama, K.Koyabu, D.Dhuyvet H.Borghys, H.Gijsen, Y.Yamano, Y.Iso, K.Kusakabe
compound source
Molecule: Beta-Secretase 1
Chain: A
Fragment: Unp Residues 43-454
Synonym: Aspartyl Protease 2,Asp 2,Beta-Site Amyloid Precur Protein Cleaving Enzyme 1,Beta-Site App Cleaving Enzyme 1,M Membrane-Associated Aspartic Protease 2;
Ec: 3.4.23.46
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace1, Bace, Kiaa1149
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 61 2 2
R_factor 0.191 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.149 102.149 171.125 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 0B6, GOL, IOD enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRational Design of Novel 1,3-Oxazine Based beta-Secretase (BACE1) Inhibitors: Incorporation of a Double Bond To Reduce P-gp Efflux Leading to Robust Abeta Reduction in the Brain., Fuchino K, Mitsuoka Y, Masui M, Kurose N, Yoshida S, Komano K, Yamamoto T, Ogawa M, Unemura C, Hosono M, Ito H, Sakaguchi G, Ando S, Ohnishi S, Kido Y, Fukushima T, Miyajima H, Hiroyama S, Koyabu K, Dhuyvetter D, Borghys H, Gijsen HJM, Yamano Y, Iso Y, Kusakabe KI, J Med Chem. 2018 May 23. doi: 10.1021/acs.jmedchem.8b00002. PMID:29733614
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (5ygy.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5YGY
  • CSU: Contacts of Structural Units for 5YGY
  • Structure Factors (348 Kb)
  • Retrieve 5YGY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YGY from S2C, [Save to disk]
  • View 5YGY 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 5YGY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ygy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YGY
  • Community annotation for 5YGY at PDBWiki (http://pdbwiki.org)

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