Structure of PDB 3i25 Chain A Binding Site BS01

Receptor Information
>3i25 Chain A (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
NLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VESQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDMV7
InChIInChI=1S/C45H55F2N5O10S/c1-28(2)41(45(57)48-26-30-13-9-7-10-14-30)51-44(56)40(61-18-17-60-5)25-39(53)38(27-62-37-23-34(46)22-35(47)24-37)50-43(55)33-19-32(20-36(21-33)52(4)63(6,58)59)42(54)49-29(3)31-15-11-8-12-16-31/h7-16,19-24,28-29,38-41,53H,17-18,25-27H2,1-6H3,(H,48,57)(H,49,54)(H,50,55)(H,51,56)/t29-,38+,39+,40-,41+/m1/s1
InChIKeyRSTFVOGBJGGSOD-NDKACYJFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C[C@H](c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)N[C@@H](COc3cc(cc(c3)F)F)[C@H](C[C@H](C(=O)N[C@@H](C(C)C)C(=O)NCc4ccccc4)OCCOC)O
CACTVS 3.370COCCO[CH](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)N[CH](C(C)C)C(=O)NCc4ccccc4
OpenEye OEToolkits 1.7.0CC(C)C(C(=O)NCc1ccccc1)NC(=O)C(CC(C(COc2cc(cc(c2)F)F)NC(=O)c3cc(cc(c3)N(C)S(=O)(=O)C)C(=O)NC(C)c4ccccc4)O)OCCOC
CACTVS 3.370COCCO[C@H](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)N[C@@H](C(C)C)C(=O)NCc4ccccc4
ACDLabs 12.01O=C(NCc1ccccc1)C(NC(=O)C(OCCOC)CC(O)C(NC(=O)c3cc(C(=O)NC(c2ccccc2)C)cc(N(C)S(=O)(=O)C)c3)COc4cc(F)cc(F)c4)C(C)C
FormulaC45 H55 F2 N5 O10 S
NameN-[(2S,3S,5R)-1-(3,5-difluorophenoxy)-3-hydroxy-5-(2-methoxyethoxy)-6-[[(2S)-3-methyl-1-oxo-1-(phenylmethylamino)butan-2-yl]amino]-6-oxo-hexan-2-yl]-5-(methyl-methylsulfonyl-amino)-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide;
N-[(1S,2S,4R)-4-((S)-1-Benzylcarbamoyl-2-methyl-propylcarbamoyl)-1-(3,5-difluoro-phenoxymethyl)-2-hydroxy-4-(2-methoxy-ethoxy)-butyl]-5-(methanesulfonyl-methyl-amino)-N'-((R)-1-phenyl-ethyl)-isophthalamide
ChEMBLCHEMBL591644
DrugBank
ZINCZINC000150344683
PDB chain3i25 Chain A Residue 531 [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]
PDB3i25 Discovery of potent BACE-1 inhibitors containing a new hydroxyethylene (HE) scaffold: exploration of P1' alkoxy residues and an aminoethylene (AE) central core
Resolution2.1 Å
Binding residue
(original residue number in PDB)
G11 Q12 G13 L30 D32 G34 S35 P70 Y71 T72 Q73 G74 F108 I110 Y198 I226 D228 G230 T231 T232 N233 R235 T329 A335
Binding residue
(residue number reindexed from 1)
G14 Q15 G16 L33 D35 G37 S38 P73 Y74 T75 Q76 G77 F111 I113 Y190 I218 D220 G222 T223 T224 N225 R227 T317 A323
Annotation score1
Binding affinityMOAD: Ki=3.1nM
PDBbind-CN: -logKd/Ki=8.51,Ki=3.1nM
BindingDB: Ki=3.1nM
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 D220 T223
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:3i25, PDBe:3i25, PDBj:3i25
PDBsum3i25
PubMed20122837
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]