Structure of PDB 5v0n Chain A Binding Site BS01

Receptor Information
>5v0n Chain A (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDE
FRTAAVEGPFVTLDMEDCGYN
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 A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		G11 L30 D32 G34 S35 Y71 T72 Q73 F108 I118 Y198 D228 G230 T231 T232 N233
Binding residue
(residue number reindexed from 1)		G13 L32 D34 G36 S37 Y73 T74 Q75 F110 I120 Y191 D221 G223 T224 T225 N226
Annotation score1
Binding affinityMOAD: Ki=67.1nM
PDBbind-CN: -logKd/Ki=7.17,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) D34 S37 N39 A41 Y73 D221 T224
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:5v0n, PDBe:5v0n, PDBj:5v0n
PDBsum5v0n
PubMed28427814
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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