3DM6 Beta-secretase 1 complexed with statine-based inhibitor date
authors Lindberg, J., Borkakoti, N., Nystrom, S.
compound source
R_Free 0.28131
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
ligand 757, IPA BindingDB enzyme
A, C, B

Primary referenceDesign, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues., Back M, Nyhlen J, Kvarnstrom I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nystrom S, Hallberg A, Rosenquist S, Samuelsson B, Bioorg Med Chem. 2008 Nov 1;16(21):9471-86. Epub 2008 Sep 19. PMID:18842420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (188 Kb) [Save to disk]
  • Biological Unit Coordinates (3dm6.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3dm6.pdb2.gz) 64 Kb
  • Biological Unit Coordinates (3dm6.pdb3.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 3DM6
  • CSU: Contacts of Structural Units for 3DM6
  • Likely Quarternary Molecular Structure file(s) for 3DM6
  • Structure Factors (774 Kb)
  • Retrieve 3DM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DM6 from S2C, [Save to disk]
  • Re-refined 3dm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DM6 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 3DM6
  • 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 3DM6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dm6_C] [3dm6] [3dm6_A] [3dm6_B]
  • 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 3DM6
  • Community annotation for 3DM6 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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