Structure of PDB 3udr Chain A Binding Site BS01

Receptor Information
>3udr 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 ID09F
InChIInChI=1S/C19H21N3O3/c20-11-18(8-4-1-5-9-18)25-16(23)15-10-19(12-21-15)13-6-2-3-7-14(13)22-17(19)24/h2-3,6-7,15,21H,1,4-5,8-10,12H2,(H,22,24)/t15-,19-/m1/s1
InChIKeyVRCMTLQTPNLTIN-DNVCBOLYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O=C1Nc2ccccc2[C]13CN[CH](C3)C(=O)OC4(CCCCC4)C#N
ACDLabs 12.01N#CC4(OC(=O)C3NCC1(c2c(NC1=O)cccc2)C3)CCCCC4
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C3(CC(NC3)C(=O)OC4(CCCCC4)C#N)C(=O)N2
CACTVS 3.370O=C1Nc2ccccc2[C@@]13CN[C@H](C3)C(=O)OC4(CCCCC4)C#N
OpenEye OEToolkits 1.7.2c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)OC4(CCCCC4)C#N)C(=O)N2
FormulaC19 H21 N3 O3
Name1-cyanocyclohexyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
ChEMBLCHEMBL2181985
DrugBank
ZINCZINC000095575049
PDB chain3udr 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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PDB3udr Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		L30 D32 G34 Y71 Q73 F108 Y198 I226 D228 G230
Binding residue
(residue number reindexed from 1)		L32 D34 G36 Y73 Q75 F110 Y194 I222 D224 G226
Annotation score1
Binding affinityMOAD: ic50=11uM
PDBbind-CN: -logKd/Ki=4.96,IC50=11uM
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:3udr, PDBe:3udr, PDBj:3udr
PDBsum3udr
PubMed22468999
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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