Structure of PDB 3udn Chain A Binding Site BS01

Receptor Information
>3udn 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 ID09B
InChIInChI=1S/C20H17N3O3/c21-10-13-5-7-14(8-6-13)11-26-18(24)17-9-20(12-22-17)15-3-1-2-4-16(15)23-19(20)25/h1-8,17,22H,9,11-12H2,(H,23,25)/t17-,20-/m1/s1
InChIKeyQVGGPTMZUCXDDT-YLJYHZDGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C3(CC(NC3)C(=O)OCc4ccc(cc4)C#N)C(=O)N2
OpenEye OEToolkits 1.7.2c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)OCc4ccc(cc4)C#N)C(=O)N2
CACTVS 3.370O=C1Nc2ccccc2[C@@]13CN[C@H](C3)C(=O)OCc4ccc(cc4)C#N
CACTVS 3.370O=C1Nc2ccccc2[C]13CN[CH](C3)C(=O)OCc4ccc(cc4)C#N
ACDLabs 12.01N#Cc1ccc(cc1)COC(=O)C4NCC2(c3c(NC2=O)cccc3)C4
FormulaC20 H17 N3 O3
Name4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
ChEMBLCHEMBL2181980
DrugBank
ZINCZINC000095573978
PDB chain3udn Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3udn Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.
Resolution2.193 Å
Binding residue
(original residue number in PDB)		L30 D32 G34 Y71 Q73 F108 R128 Y198 D228 G230
Binding residue
(residue number reindexed from 1)		L32 D34 G36 Y73 Q75 F110 R130 Y194 D224 G226
Annotation score1
Binding affinityMOAD: ic50=7uM
PDBbind-CN: -logKd/Ki=5.15,IC50=7.0uM
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:3udn, PDBe:3udn, PDBj:3udn
PDBsum3udn
PubMed22468999
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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