Structure of PDB 3udh Chain A Binding Site BS01

Receptor Information
>3udh 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 ID091
InChIInChI=1S/C11H12N2O/c14-10-11(5-6-12-7-11)8-3-1-2-4-9(8)13-10/h1-4,12H,5-7H2,(H,13,14)/t11-/m1/s1
InChIKeyFQSHLSLQUHZOMV-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C3(CCNC3)C(=O)N2
OpenEye OEToolkits 1.7.2c1ccc2c(c1)[C@]3(CCNC3)C(=O)N2
CACTVS 3.370O=C1Nc2ccccc2[C@]13CCNC3
ACDLabs 12.01O=C2Nc1c(cccc1)C23CCNC3
CACTVS 3.370O=C1Nc2ccccc2[C]13CCNC3
FormulaC11 H12 N2 O
Name(3S)-spiro[indole-3,3'-pyrrolidin]-2(1H)-one
ChEMBLCHEMBL2181988
DrugBank
ZINCZINC000095577096
PDB chain3udh Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3udh Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		L30 D32 Y71 Q73 F108 D228 G230
Binding residue
(residue number reindexed from 1)		L32 D34 Y73 Q75 F110 D224 G226
Annotation score1
Binding affinityMOAD: Kd=1.4mM
PDBbind-CN: -logKd/Ki=2.85,Kd=1.4mM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3udh, PDBe:3udh, PDBj:3udh
PDBsum3udh
PubMed22468999
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]