Structure of PDB 3duy Chain B Binding Site BS01

Receptor Information
>3duy Chain B (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEIN
GQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPD
GFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPV
EDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEF
RTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDAFJ
InChIInChI=1S/C25H49N3O4S/c1-8-9-13-26-24(31)19(6)16-22(29)21(15-18(4)5)28-25(32)20(12-14-33-7)27-23(30)11-10-17(2)3/h17-22,29H,8-16H2,1-7H3,(H,26,31)(H,27,30)(H,28,32)/t19-,20+,21+,22+/m1/s1
InChIKeyXTRMRNMVFXWTCC-MLNNCEHLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCNC(=O)[C@H](C)C[C@H](O)[C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)CCC(C)C
OpenEye OEToolkits 1.5.0CCCCNC(=O)C(C)CC(C(CC(C)C)NC(=O)C(CCSC)NC(=O)CCC(C)C)O
OpenEye OEToolkits 1.5.0CCCCNC(=O)[C@H](C)C[C@@H]([C@H](CC(C)C)NC(=O)[C@H](CCSC)NC(=O)CCC(C)C)O
CACTVS 3.341CCCCNC(=O)[CH](C)C[CH](O)[CH](CC(C)C)NC(=O)[CH](CCSC)NC(=O)CCC(C)C
ACDLabs 10.04O=C(NC(C(=O)NC(CC(C)C)C(O)CC(C(=O)NCCCC)C)CCSC)CCC(C)C
FormulaC25 H49 N3 O4 S
Name(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide;
(2R,4S,5S)-4-Hydroxy-2,7-dimethyl-5-[(S)-2-(4-methyl-pentanoylamino)-4-methylsulfanyl-butyrylamino]-octanoic acid butylamide
ChEMBLCHEMBL461606
DrugBank
ZINCZINC000039145436
PDB chain3duy Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3duy Structure-based design and synthesis of macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		G13 L30 D32 G34 Y71 T72 Q73 F108 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		G16 L33 D35 G37 Y74 T75 Q76 F111 D219 G221 T222 T223
Annotation score1
Binding affinityMOAD: ic50=1.4uM
BindingDB: IC50=>10000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D219 T222
Enzyme Commision number 3.4.23.46: memapsin 2.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3duy, PDBe:3duy, PDBj:3duy
PDBsum3duy
PubMed19195886
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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