Structure of PDB 3udk Chain A Binding Site BS01

Receptor Information
>3udk Chain A (length=394) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGASEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIV
RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASST
EKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQ
YLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGF
AVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESRSHHHH
Ligand information
Ligand ID095
InChIInChI=1S/C17H20N2O4/c20-15(23-11-5-7-22-8-6-11)14-9-17(10-18-14)12-3-1-2-4-13(12)19-16(17)21/h1-4,11,14,18H,5-10H2,(H,19,21)/t14-,17-/m1/s1
InChIKeyHIOAPSYSJQPIRC-RHSMWYFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C3(CC(NC3)C(=O)OC4CCOCC4)C(=O)N2
OpenEye OEToolkits 1.7.2c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)OC4CCOCC4)C(=O)N2
CACTVS 3.370O=C(OC1CCOCC1)[CH]2C[C]3(CN2)C(=O)Nc4ccccc34
CACTVS 3.370O=C(OC1CCOCC1)[C@H]2C[C@]3(CN2)C(=O)Nc4ccccc34
ACDLabs 12.01O=C(OC1CCOCC1)C4NCC3(c2ccccc2NC3=O)C4
FormulaC17 H20 N2 O4
Nametetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
ChEMBLCHEMBL2181998
DrugBank
ZINCZINC000095577682
PDB chain3udk Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3udk Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.
Resolution2.51 Å
Binding residue
(original residue number in PDB)		L30 D32 G34 Y71 I226 D228 V332
Binding residue
(residue number reindexed from 1)		L32 D34 G36 Y73 I222 D224 V328
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.49,IC50=32uM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D224 T227
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:3udk, PDBe:3udk, PDBj:3udk
PDBsum3udk
PubMed22468999
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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