2VKM Hydrolase date Dec 04, 2007
title Crystal Structure Of Grl-8234 Bound To Bace (Beta-Secretase)
authors L.Hong, J.Tang, A.K.Ghosh
compound source
Molecule: Beta-Secretase 1
Chain: A, B, C, D
Fragment: Beta-Secretase Catalytic Domain, Residues 58-446
Synonym: Beta-Site App Cleaving Enzyme 1, Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1, Membrane-Associated Aspartic Protease 2, Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2, Bace;
Engineered: Yes
Other_details: Beta Secretase Inhibitor
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 1 21 1
R_factor 0.2016 R_Free 0.2418
length a length b length c angle alpha angle beta angle gamma
86.704 130.308 87.711 90.00 97.41 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand BSD BindingDB enzyme
A, D, C, B

Primary referencePotent memapsin 2 (beta-secretase) inhibitors: design, synthesis, protein-ligand X-ray structure, and in vivo evaluation., Ghosh AK, Kumaragurubaran N, Hong L, Kulkarni S, Xu X, Miller HB, Reddy DS, Weerasena V, Turner R, Chang W, Koelsch G, Tang J, Bioorg Med Chem Lett. 2008 Feb 1;18(3):1031-6. Epub 2008 Jan 3. PMID:18180160
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (272 Kb) [Save to disk]
  • Biological Unit Coordinates (2vkm.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (2vkm.pdb2.gz) 71 Kb
  • Biological Unit Coordinates (2vkm.pdb3.gz) 71 Kb
  • Biological Unit Coordinates (2vkm.pdb4.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 2VKM
  • CSU: Contacts of Structural Units for 2VKM
  • Likely Quarternary Molecular Structure file(s) for 2VKM
  • Structure Factors (1684 Kb)
  • Retrieve 2VKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VKM from S2C, [Save to disk]
  • Re-refined 2vkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VKM 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 2VKM
  • 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 2VKM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vkm_C] [2vkm_B] [2vkm_D] [2vkm] [2vkm_A]
  • 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 2VKM
  • Community annotation for 2VKM 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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