4FGX Hydrolase Hydrolase Inhibitor date Jun 05, 2012
title Crystal Structure Of Bace1 With Novel Inhibitor
authors T.T.Chen, W.Y.Chen, L.Li, Y.C.Xu
compound source
Molecule: Beta-Secretase 1
Chain: A
Synonym: Aspartyl Protease 2, Asp2, Asp 2, Beta-Site Amyloi Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Memapsin-2, Membrane-Associated Aspartic Protease 2;
Ec: 3.4.23.46
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace, Bace1, Kiaa1149
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Inhibitor (2r,5s,8s,12s,13s,16s,19s,22s)-16-(3-Am Oxopropyl)-2,13-Dibenzyl-12,22-Dihydroxy-8-Isobutyl-19-Isop 17-Trimethyl-4,7,10,15,18,21-Hexaoxo-3,6,9,14,17,20-Hexaaza 1-Oic Acid;
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.167 R_Free 0.181
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.710 128.730 76.160 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.59 Å
ligand 2OP, GNC, PEG, PSA, SO4, URE, ZAE enzyme Hydrolase E.C.3.4.23.46 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases., Liu Y, Zhang W, Li L, Salvador LA, Chen T, Chen W, Felsenstein KM, Ladd TB, Price AR, Golde TE, He J, Xu Y, Li Y, Luesch H, J Med Chem. 2012 Dec 13;55(23):10749-65. doi: 10.1021/jm301630s. Epub 2012 Nov, 26. PMID:23181502
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (4fgx.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (4fgx.pdb2.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 4FGX
  • CSU: Contacts of Structural Units for 4FGX
  • Structure Factors (538 Kb)
  • Retrieve 4FGX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FGX from S2C, [Save to disk]
  • Re-refined 4fgx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FGX 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 4FGX
  • 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 4FGX, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fgx_B] [4fgx_A] [4fgx]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4FGX
  • Community annotation for 4FGX at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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