Structure of PDB 3udp Chain A Binding Site BS01

Receptor Information
>3udp 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 ID09D
InChIInChI=1S/C21H19BrN2O3S/c22-12-5-6-18-13(9-12)17(7-8-28-18)27-19(25)16-10-21(11-23-16)14-3-1-2-4-15(14)24-20(21)26/h1-6,9,16-17,23H,7-8,10-11H2,(H,24,26)/t16-,17+,21-/m1/s1
InChIKeyOPUJSFZMYKHRTH-LLGFUMIMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)O[C@H]4CCSc5c4cc(cc5)Br)C(=O)N2
CACTVS 3.370Brc1ccc2SCC[CH](OC(=O)[CH]3C[C]4(CN3)C(=O)Nc5ccccc45)c2c1
CACTVS 3.370Brc1ccc2SCC[C@H](OC(=O)[C@H]3C[C@]4(CN3)C(=O)Nc5ccccc45)c2c1
ACDLabs 12.01O=C2Nc1ccccc1C23CC(NC3)C(=O)OC4c5c(SCC4)ccc(Br)c5
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C3(CC(NC3)C(=O)OC4CCSc5c4cc(cc5)Br)C(=O)N2
FormulaC21 H19 Br N2 O3 S
Name(4S)-6-bromo-3,4-dihydro-2H-thiochromen-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
ChEMBL
DrugBank
ZINCZINC000095579712
PDB chain3udp 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

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PDB3udp 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 T72 Q73 F108 R128 Y198 D228 G230
Binding residue
(residue number reindexed from 1)		L32 D34 G36 Y73 T74 Q75 F110 R130 Y194 D224 G226
Annotation score1
Binding affinityMOAD: ic50=6uM
PDBbind-CN: -logKd/Ki=5.22,IC50=6.0uM
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:3udp, PDBe:3udp, PDBj:3udp
PDBsum3udp
PubMed22468999
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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