2VNM Hydrolase date Feb 05, 2008
title Human Bace-1 In Complex With 3-(1,1-Dioxidotetrahydro-2h-1,2 2-Yl)-5-(Ethylamino)-N-((1s,2r)-2-Hydroxy-1-(Phenylmethyl)- (Trifluoromethyl)Phenyl)Methyl)Amino)Propyl)Benzamide
authors N.Charrier, B.Clarke, L.Cutler, E.Demont, C.Dingwall, R.Dunsdon, P J.Hawkins, C.Howes, I.Hussain, P.Jeffrey, G.Maile, R.Matico, J.Mo A.Naylor, A.Obrien, S.Redshaw, P.Rowland, V.Soleil, K.J.Smith, S. P.Theobald, D.Vesey, D.S.Walter, G.Wayne
compound source
Molecule: Beta-Secretase 1
Chain: A
Fragment: Residues 61-452
Synonym: Bace-1, Beta-Site App Cleaving Enzyme 1, Beta-Site Precursor Protein Cleaving Enzyme 1, Membrane-Associated As Protease 2, Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2;
Ec: 3.4.23.46
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Cho
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.952 76.217 104.492 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand CM8 BindingDB enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSecond Generation of Hydroxyethylamine BACE-1 Inhibitors: Optimizing Potency and Oral Bioavailability., Charrier N, Clarke B, Cutler L, Demont E, Dingwall C, Dunsdon R, East P, Hawkins J, Howes C, Hussain I, Jeffrey P, Maile G, Matico R, Mosley J, Naylor A, O'Brien A, Redshaw S, Rowland P, Soleil V, Smith KJ, Sweitzer S, Theobald P, Vesey D, Walter DS, Wayne G, J Med Chem. 2008 May 6;. PMID:18457381
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (2vnm.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 2VNM
  • CSU: Contacts of Structural Units for 2VNM
  • Likely Quarternary Molecular Structure file(s) for 2VNM
  • Structure Factors (268 Kb)
  • Retrieve 2VNM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VNM from S2C, [Save to disk]
  • Re-refined 2vnm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VNM 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 2VNM
  • 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
  • 3D motif for 2VNM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vnm_A] [2vnm]
  • SWISS-PROT database: [P56817]
  • Belongs to the β-amyloid cleaving enzyme (bace1) family according to TCDB.
  • Domain organization of [BACE1_HUMAN] by SWISSPFAM
  • Other resources with information on 2VNM
  • Community annotation for 2VNM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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