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Design and Synthesis of BACE1 Inhibitors with In Vivo Brain Reduction of beta-Amyloid Peptides (COMPOUND (R)-41)
4B00
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase
    Structure Weight: 46535.63
    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: Gene View for BACE1 BACE KIAA1149
    UniProtKB: Protein Feature View | Search PDB | P56817  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   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) 
    4B05  PRECLINICAL CHARACTERIZATION OF AZD3839, A NOVEL CLINICAL CANDIDATE BACE1 INHIBITOR FOR THE TREATMENT OF ALZHEIMER DISEASE 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    ACT
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    ACT C2 H3 O2
    ACETATE ION
    I6X
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    I6X C30 H25 F N4 O
    5-{(1R)-3-amino-4-fluoro-1-[3-(5-prop-1-yn- 1-ylpyridin-3-yl)phenyl]-1H-isoindol-1-yl}- 1-ethyl-3-methylpyridin-2(1H)-one
    I6X:4B00
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    I6X
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    I6X
    IC50: 0.16 - 2.6 nM (97 - 99) - data from BindingDB  
    IC50: 2.44 nM - data from BindingMOAD  
    IC50: 2.44 nM - data from PDBbind  
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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