Preclinical characterization of AZD3839, a novel clinical candidate BACE1 inhibitor for the treatment of Alzheimer Disease DOI:10.2210/pdb4b05/pdb

4B05   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Hydrolase Structure Weight: 46572.53 Molecule: BETA-SECRETASE 1 Polymer: 1 Type: protein Length: 411 Chains: A EC#: 3.4.23.46    Fragment: RESIDUES 43-453 Mutation: YES Organism Homo sapiens Gene Names BACE1 BACE KIAA1149 UniProtKB:   Protein Feature View | Search PDB | P56817         Source Hide Polymer: 1 Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli       Related PDB Entries Hide Identifier Details 1FKN  STRUCTURE OF BETA-SECRETASE COMPLEXED WITH INHIBITOR  1M4H  CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITHINHIBITOR OM00-3  1PY1  COMPLEX OF GGA1-VHS DOMAIN AND BETA-SECRETASE C- TERMINALPHOSPHOPEPTIDE  1SGZ  CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE CATALYTICDOMAIN.  1TQF  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-124,671  1UJJ  VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C-TERMINAL PEPTIDEFROM BACE  1UJK  VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C- TERMINALPHOSPHOPEPTIDE FROM BACE  1W50  APO STRUCTURE OF BACE (BETA SECRETASE)  1W51  BACE (BETA SECRETASE) IN COMPLEX WITH A NANOMOLAR NON -PEPTIDIC INHIBITOR  1XN2  NEW SUBSTRATE BINDING POCKETS FOR BETA-SECRETASE.  1XN3  CRYSTAL STRUCTURE OF BETA-SECRETASE BOUND TO A LONGINHIBITOR WITH ADDITIONAL UPSTREAM RESIDUES.  1XS7  CRYSTAL STRUCTURE OF A CYCLOAMIDE-URETHANE-DERIVED NOVELINHIBITOR BOUND TO HUMAN BRAIN MEMAPSIN 2 (BETA- SECRETASE).  1YM2  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AUR200  1YM4  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AMK640  2B8L  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-000384950  2B8V  CRYSTAL STRUCTURE OF HUMAN BETA-SECRETASE COMPLEXED WITH L-L000430,469  2FDP  CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITH AN AMINO-ETHYLENE INHIBITOR  2VA5  X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 8C  2VA6  X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 24  2VA7  X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 27  2VIE  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-1-BENZYL- 2-HYDROXY-3-((1,1,5-TRIMETHYLHEXYL)AMINO)PROPYL)-3 -(ETHYLAMINO)-5-(2-OXOPYRROLIDIN-1-YL)BENZAMIDE  2VIJ  HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- DIOXIDOTETRAHYDRO-2H-1,2-THIAZIN-2-YL)-5-(ETHYLAMINO )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(1,2,3 ,4-TETRAHYDRO-1-NAPHTHALENYLAMINO)PROPYL)BENZAMIDE  2VIY  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(PENTYLSULFONYL) BENZAMIDE  2VIZ  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(2-OXO-1- PYRROLIDINYL)-5-(PROPYLOXY)BENZAMIDE  2VJ6  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- OXO-1-PYRROLIDINYL)BENZAMIDE  2VJ7  HUMAN BACE-1 IN COMPLEX WITH 3-(ETHYLAMINO)-N-((1S, 2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)-5-(2-OXO-1-PYRROLIDINYL) BENZAMIDE  2VJ9  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-( CYCLOHEXYLAMINO)-2-HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-( ETHYLAMINO)-5-(2-OXO-1-PYRROLIDINYL)BENZAMIDE  2VKM  CRYSTAL STRUCTURE OF GRL-8234 BOUND TO BACE (BETA- SECRETASE)  2VNM  HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- DIOXIDOTETRAHYDRO-2H-1,2-THIAZIN-2-YL)-5-(ETHYLAMINO )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-( TRIFLUOROMETHYL)PHENYL)METHYL)AMINO)PROPYL)BENZAMIDE  2VNN  HUMAN BACE-1 IN COMPLEX WITH 7-ETHYL-N-((1S,2R)- 2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)-1-METHYL-3,4-DIHYDRO-1H -(1,2,5)THIADIAZEPINO(3,4,5-HI)INDOLE-9- CARBOXAMIDE 2,2-DIOXIDE  2WEZ  HUMAN BACE-1 IN COMPLEX WITH 1-ETHYL-N-((1S,2R)- 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-4-(2-OXO-1-PYRROLIDINYL)-1H- INDOLE-6-CARBOXAMIDE  2WF0  HUMAN BACE-1 IN COMPLEX WITH 4-ETHYL-N-((1S,2R)- 2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)-8-(2-OXO-1-PYRROLIDINYL)- 6-QUINOLINECARBOXAMIDE  2WF1  HUMAN BACE-1 IN COMPLEX WITH 7-ETHYL-N-((1S,2R)- 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL(METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-1-METHYL-3,4-DIHYDRO-1H-(1,2, 5)THIADIAZEPINO(3,4,5-HI)INDOLE-9-CARBOXAMIDE 2,2 -DIOXIDE  2WF2  HUMAN BACE-1 IN COMPLEX WITH 8-ETHYL-N-((1S,2R)- 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-1-METHYL-3,4,7,8-TETRAHYDRO-1H ,6H-(1,2,5)THIADIAZEPINO(5,4,3-DE)QUINOXALINE-10 -CARBOXAMIDE 2,2-DIOXIDE  2WF3  HUMAN BACE-1 IN COMPLEX WITH 6-(ETHYLAMINO)-N-((1S, 2R)-2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)- 1-(PHENYLMETHYL)PROPYL)-1-METHYL-1,3,4,5-TETRAHYDRO -2,1-BENZOTHIAZEPINE-8-CARBOXAMIDE 2,2-DIOXIDE  2WF4  HUMAN BACE-1 IN COMPLEX WITH 6-ETHYL-1-METHYL-N -((1S)-2-OXO-1-(PHENYLMETHYL)-3-(TETRAHYDRO-2H-PYRAN -4-YLAMINO)PROPYL)-1,3,4,6-TETRAHYDRO(1,2) THIAZEPINO(5,4,3-CD)INDOLE-8-CARBOXAMIDE 2,2- DIOXIDE  2WJO  HUMAN BACE (BETA SECRETASE) IN COMPLEX WITH CYCLOHEXANECARBOXYLIC ACID (2-(2-AM INO-6-PHENOXY-4H- QUINAZOLIN-3-YL)-2 -CYCLOHEXYL-ETHYL)-AMIDE  2XFI  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-((METHYLSULFONYL)(PHENYL )AMINO)BENZAMIDE  2XFJ  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- OXO-1-PYRROLIDINYL)BENZAMIDE  2XFK  HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(( METHYLSULFONYL)(PHENYL)AMINO)BENZAMIDE  4ACU  AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 14  4ACX  AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 23  4AZY  DESIGN AND SYNTHESIS OF BACE1 INHIBITORS WITH IN VIVO BRAIN REDUCTION OF BETA-AMYLOID PEPTIDES (COMPOUND 10)  4B00  DESIGN AND SYNTHESIS OF BACE1 INHIBITORS WITH IN VIVO BRAIN REDUCTION OF BETA-AMYLOID PEPTIDES (COMPOUND (R )-41)      Ligand Chemical Component Hide Identifier Formula Name Interactions 32D Search  Download  C24 H16 F3 N5 (1S)-1-[2-(difluoromethyl)pyridin-4-yl]-4- fluoro-1-(3-pyrimidin-5-ylphenyl)-1H-isoindol- 3-amine   Ligand Explorer ACT Search  Download  C2 H3 O2 ACETATE ION   Ligand Explorer NA Search  Download  Na SODIUM ION   Ligand Explorer     External Domain Annotations Hide Pfam Classification: 1 Domain - data from Pfam       Structural Biology Knowledgebase Data Hide     Data in orange boxes are gathered from external resources (when available). Reset Layout

Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Jeppsson, F.,  Eketjall, S.,  Janson, J.,  Karlstrom, S.,  Gustavsson, S.,  Olsson, L.L.,  Radesater, A.C.,  Ploeger, B.,  Cebers, G.,  Kolmodin, K.,  Swahn, B.M.,  Von Berg, S.,  Bueters, T.,  Falting, J. Deposition:   2012-06-28 Release:   2012-10-17 Last Modified (REVDAT):   2012-12-19     Revision History    Hide Mouse over text for details 2012-12-19 Citation 2012-12-19 Refinement description 2012-12-12 Citation 2012-10-24 Citation     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   1.80 R-Value: 0.180 (obs.) R-Free: 0.215 Space Group: P 21 21 21 Unit Cell:   Length [Å] Angles [°] a = 47.53 α = 90.00  b = 76.53 β = 90.00  c = 104.16 γ = 90.00      Molecule of the Month Hide beta-Secretase Amyloid-beta Precursor Protein