Structure of PDB 5v0n Chain B Binding Site BS01

Receptor Information
>5v0n Chain B (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGFPASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIV
RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASST
EKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQ
YLRPVDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID8W4
InChIInChI=1S/C36H43N5O5S/c1-5-26-22-41-23-36(2,3)47(45,46)39(4)30-20-27(19-28(26)32(30)41)34(43)38-29(18-24-12-8-6-9-13-24)33(42)31-35(44)40(17-16-37-31)21-25-14-10-7-11-15-25/h6-15,19-20,22,29,31,33,37,42H,5,16-18,21,23H2,1-4H3,(H,38,43)/t29-,31-,33-/m0/s1
InChIKeyWBWSVNAKBNLSOJ-WXWREJFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCc1cn2c3c1cc(cc3N(S(=O)(=O)C(C2)(C)C)C)C(=O)NC(Cc4ccccc4)C(C5C(=O)N(CCN5)Cc6ccccc6)O
ACDLabs 12.01c1c(cccc1)CC(NC(=O)c2cc4c3c(c2)c(CC)cn3CC(S(=O)(N4C)=O)(C)C)C(C6NCCN(Cc5ccccc5)C6=O)O
OpenEye OEToolkits 2.0.6CCc1cn2c3c1cc(cc3N(S(=O)(=O)C(C2)(C)C)C)C(=O)N[C@@H](Cc4ccccc4)[C@@H]([C@H]5C(=O)N(CCN5)Cc6ccccc6)O
CACTVS 3.385CCc1cn2CC(C)(C)[S](=O)(=O)N(C)c3cc(cc1c23)C(=O)N[C@@H](Cc4ccccc4)[C@H](O)[C@@H]5NCCN(Cc6ccccc6)C5=O
CACTVS 3.385CCc1cn2CC(C)(C)[S](=O)(=O)N(C)c3cc(cc1c23)C(=O)N[CH](Cc4ccccc4)[CH](O)[CH]5NCCN(Cc6ccccc6)C5=O
FormulaC36 H43 N5 O5 S
NameN-{(1S,2S)-1-[(2S)-4-benzyl-3-oxopiperazin-2-yl]-1-hydroxy-3-phenylpropan-2-yl}-7-ethyl-1,3,3-trimethyl-2,2-dioxo-1,2,3,4-tetrahydro-2lambda~6~-[1,2,5]thiadiazepino[3,4,5-hi]indole-9-carboxamide
ChEMBLCHEMBL4065655
DrugBank
ZINC
PDB chain5v0n Chain B Residue 406 [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]
PDB5v0n Design, synthesis, and X-ray structural studies of BACE-1 inhibitors containing substituted 2-oxopiperazines as P1'-P2' ligands.
Resolution2.155 Å
Binding residue
(original residue number in PDB)		D32 G34 S35 Y71 T72 Q73 F108 Y198 D228 G230 T232 N233 R235
Binding residue
(residue number reindexed from 1)		D35 G37 S38 Y74 T75 Q76 F111 Y194 D224 G226 T228 N229 R231
Annotation score1
Binding affinityMOAD: Ki=67.1nM
BindingDB: Ki=67nM,EC50=19nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 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:5v0n, PDBe:5v0n, PDBj:5v0n
PDBsum5v0n
PubMed28427814
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]