3UDY Hydrolase Hydrolase Inhibitor date Oct 28, 2011
title Crystal Structure Of Bace With Compound 11
authors I.V.Efremov, F.F.Vajdos, K.Borzilleri, S.Capetta, P.Dorff, J.Dutr M.Mansour, C.Oborski, T.O'Connell, T.J.O'Sullivan, J.Pandit, H.W J.Withka
compound source
Molecule: Beta-Secretase 1
Chain: A
Fragment: Unp Residues 58-453
Synonym: Bace, Aspartyl Protease 2, Asp2, Asp 2, Beta-Site Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Memapsin-2, Membrane-Associated Aspartic Protease 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace1, Bace, Kiaa1149
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.308
length a length b length c angle alpha angle beta angle gamma
74.690 103.964 99.406 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 09G, EDO, PEG, ZN BindingDB enzyme Hydrolase E.C. BRENDA

Primary referenceDiscovery and Optimization of a Novel Spiro-pyrrolidine Inhibitors of beta-Secretase (BACE1) Through Fragment Based Drug Design., Efremov IV, Vajdos FF, Borzilleri K, Capetta S, Dorff PH, Dutra JK, Mansour M, Chen H, Goldstein SW, Noell S, Oborski CE, O'Connell TN, O'Sullivan TJ, Pandit J, Wang H, Wei B, Withka JM, McColl A, J Med Chem. 2012 Apr 2. PMID:22468999
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3udy.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3UDY
  • CSU: Contacts of Structural Units for 3UDY
  • Structure Factors (389 Kb)
  • Retrieve 3UDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UDY from S2C, [Save to disk]
  • Re-refined 3udy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UDY 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 3UDY
  • 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 3UDY, from MSDmotif at EBI
  • Fold representative 3udy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3udy_A] [3udy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3UDY
  • Community annotation for 3UDY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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