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Receptor Information

>2vkm Chain A (length=389) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFD
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN

Ligand ID

BSD

InChI

InChI=1S/C36H42N4O6S/c1-25(28-15-9-6-10-16-28)38-35(42)29-20-30(22-31(21-29)40(2)47(4,44)45)36(43)39-33(19-26-12-7-5-8-13-26)34(41)24-37-23-27-14-11-17-32(18-27)46-3/h5-18,20-22,25,33-34,37,41H,19,23-24H2,1-4H3,(H,38,42)(H,39,43)/t25-,33+,34-/m1/s1

InChIKey

HIQWWDCRULXYDF-SWROZOJRSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C[C@H](c1ccccc1)NC(=O)c2cc(cc(c2)[N@@](C)S(=O)(=O)C)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CNCc4cccc(c4)OC)O
CACTVS 3.341	COc1cccc(CNC[CH](O)[CH](Cc2ccccc2)NC(=O)c3cc(cc(c3)C(=O)N[CH](C)c4ccccc4)N(C)[S](C)(=O)=O)c1
CACTVS 3.341	COc1cccc(CNC[C@@H](O)[C@H](Cc2ccccc2)NC(=O)c3cc(cc(c3)C(=O)N[C@H](C)c4ccccc4)N(C)[S](C)(=O)=O)c1
OpenEye OEToolkits 1.5.0	CC(c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)NC(Cc3ccccc3)C(CNCc4cccc(c4)OC)O
ACDLabs 10.04	O=S(=O)(N(c2cc(cc(C(=O)NC(c1ccccc1)C)c2)C(=O)NC(Cc3ccccc3)C(O)CNCc4cc(OC)ccc4)C)C

Formula

C36 H42 N4 O6 S

Name

N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide

PDB chain

2vkm Chain A Residue 1386 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2vkm Potent Memapsin 2 (Beta-Secretase) Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure, and in Vivo Evaluation.
Resolution	2.05 Å
Binding residue (original residue number in PDB)	Q12 G13 L30 D32 G34 S35 Y71 T72 Q73 F108 W115 I118 D228 G230 T231 T232 N233 R235
Binding residue (residue number reindexed from 1)	Q16 G17 L34 D36 G38 S39 Y75 T76 Q77 F112 W119 I122 D232 G234 T235 T236 N237 R239
Annotation score	1
Binding affinity	MOAD: Ki=1.8nM PDBbind-CN: -logKd/Ki=8.74,Ki=1.8nM BindingDB: IC50=1nM,Ki=1.8nM

Catalytic site (original residue number in PDB)	D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1)	D36 S39 N41 A43 Y75 D232 T235
Enzyme Commision number	3.4.23.46: memapsin 2.

	Molecular Function
GO:0004190	aspartic-type endopeptidase activity

	Biological Process
GO:0006508	proteolysis

	Cellular Component
GO:0016020	membrane

PDB	RCSB:2vkm, PDBe:2vkm, PDBj:2vkm
PDBsum	2vkm
PubMed	18180160
UniProt	P56817\|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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Structure of PDB 2vkm Chain A Binding Site BS01