Structure of PDB 3dm6 Chain B Binding Site BS01

Receptor Information
>3dm6 Chain B (length=368) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEING
QDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDG
FWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE
SQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDE
FRTAAVEGPFVTLDCGYN
Ligand information
Ligand ID757
InChIInChI=1S/C42H45F2N5O12S/c1-22(2)37(40(54)46-31-13-27(41(55)56)12-28(14-31)42(57)58)48-36(51)20-35(50)34(21-61-33-18-29(43)17-30(44)19-33)47-39(53)26-11-25(15-32(16-26)49(4)62(5,59)60)38(52)45-23(3)24-9-7-6-8-10-24/h6-19,22-23,34-35,37,50H,20-21H2,1-5H3,(H,45,52)(H,46,54)(H,47,53)(H,48,51)(H,55,56)(H,57,58)/t23-,34+,35-,37+/m1/s1
InChIKeyXYKCBRCSBVZGIL-WRXYKUNKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)Nc1cc(cc(c1)C(=O)O)C(=O)O)NC(=O)CC(C(COc2cc(cc(c2)F)F)NC(=O)c3cc(cc(c3)N(C)S(=O)(=O)C)C(=O)NC(C)c4ccccc4)O
ACDLabs 10.04O=C(O)c1cc(cc(C(=O)O)c1)NC(=O)C(NC(=O)CC(O)C(NC(=O)c3cc(N(C)S(=O)(=O)C)cc(C(=O)NC(c2ccccc2)C)c3)COc4cc(F)cc(F)c4)C(C)C
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)Nc1cc(cc(c1)C(=O)O)C(=O)O)NC(=O)C[C@H]([C@H](COc2cc(cc(c2)F)F)NC(=O)c3cc(cc(c3)N(C)S(=O)(=O)C)C(=O)N[C@H](C)c4ccccc4)O
CACTVS 3.341CC(C)[CH](NC(=O)C[CH](O)[CH](COc1cc(F)cc(F)c1)NC(=O)c2cc(cc(c2)C(=O)N[CH](C)c3ccccc3)N(C)[S](C)(=O)=O)C(=O)Nc4cc(cc(c4)C(O)=O)C(O)=O
CACTVS 3.341CC(C)[C@H](NC(=O)C[C@@H](O)[C@H](COc1cc(F)cc(F)c1)NC(=O)c2cc(cc(c2)C(=O)N[C@H](C)c3ccccc3)N(C)[S](C)(=O)=O)C(=O)Nc4cc(cc(c4)C(O)=O)C(O)=O
FormulaC42 H45 F2 N5 O12 S
Name
ChEMBL
DrugBank
ZINCZINC000150341421
PDB chain3dm6 Chain B Residue 1000 [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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PDB3dm6 Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 D32 G34 S35 P70 Y71 T72 Q73 G74 F108 W115 Y198 D228 G230 T231 T232 N233 R235
Binding residue
(residue number reindexed from 1)		G14 Q15 G16 D35 G37 S38 P73 Y74 T75 Q76 G77 F111 W118 Y188 D218 G220 T221 T222 N223 R225
Annotation score1
Binding affinityBindingDB: IC50=37nM
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 D218 T221
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dm6, PDBe:3dm6, PDBj:3dm6
PDBsum3dm6
PubMed18842420
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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