Structure of PDB 3vv8 Chain A Binding Site BS01

Receptor Information
>3vv8 Chain A (length=358) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEIN
GQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTFPDGF
WLGEQLVCWNIFPVISLYLMGEVTNQSFRITILPQQYLRPDCYKFAISQS
STGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTL
DMEDCGYN
Ligand information
Ligand IDB02
InChIInChI=1S/C21H21N3O/c1-13-4-3-5-16(10-13)14-6-8-15(9-7-14)17-11-18(17)19-12-20(25)24(2)21(22)23-19/h3-10,12,17-18H,11H2,1-2H3,(H2,22,23)/t17-,18-/m0/s1
InChIKeySTUBOTPNCNDBOA-ROUUACIJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cccc(c1)c2ccc(cc2)[C@@H]3C[C@@H]3C4=CC(=O)N(C(=N4)N)C
OpenEye OEToolkits 1.7.6Cc1cccc(c1)c2ccc(cc2)C3CC3C4=CC(=O)N(C(=N4)N)C
CACTVS 3.370CN1C(=NC(=CC1=O)[CH]2C[CH]2c3ccc(cc3)c4cccc(C)c4)N
CACTVS 3.370CN1C(=NC(=CC1=O)[C@H]2C[C@H]2c3ccc(cc3)c4cccc(C)c4)N
ACDLabs 12.01O=C1C=C(N=C(N)N1C)C4CC4c3ccc(c2cccc(c2)C)cc3
FormulaC21 H21 N3 O
Name2-amino-3-methyl-6-[(1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl]pyrimidin-4(3H)-one
ChEMBLCHEMBL2169939
DrugBank
ZINCZINC000095553010
PDB chain3vv8 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vv8 Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D32 Y71 F108 I118 D228 G230
Binding residue
(residue number reindexed from 1)		D34 Y73 F110 I120 D219 G221
Annotation score1
Binding affinityMOAD: ic50=17.1uM
PDBbind-CN: -logKd/Ki=4.77,IC50=17.1uM
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 D219 T222
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:3vv8, PDBe:3vv8, PDBj:3vv8
PDBsum3vv8
PubMed22998419
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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