Structure of PDB 3vv6 Chain A Binding Site BS01

Receptor Information
>3vv6 Chain A (length=360) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEFPD
GFWLGEQLVCNIFPVISLYLMGEVTNQSFRITILPQQYLRPVDCYKFAIS
QSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFV
TLDMEDCGYN
Ligand information
Ligand IDB00
InChIInChI=1S/C14H15N3O/c1-17-13(18)8-12(16-14(17)15)11-7-10(11)9-5-3-2-4-6-9/h2-6,8,10-11H,7H2,1H3,(H2,15,16)/t10-,11-/m0/s1
InChIKeyVTVXXFGROBMFAL-QWRGUYRKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1C(=NC(=CC1=O)[CH]2C[CH]2c3ccccc3)N
OpenEye OEToolkits 1.7.6CN1C(=O)C=C(N=C1N)C2CC2c3ccccc3
OpenEye OEToolkits 1.7.6CN1C(=O)C=C(N=C1N)[C@H]2C[C@H]2c3ccccc3
CACTVS 3.370CN1C(=NC(=CC1=O)[C@H]2C[C@H]2c3ccccc3)N
ACDLabs 12.01O=C1C=C(N=C(N)N1C)C3CC3c2ccccc2
FormulaC14 H15 N3 O
Name2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one
ChEMBLCHEMBL2169926
DrugBank
ZINCZINC000095553844
PDB chain3vv6 Chain A Residue 510 [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]
PDB3vv6 Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode
Resolution2.05 Å
Binding residue
(original residue number in PDB)		D32 Y71 F108 I118 D228
Binding residue
(residue number reindexed from 1)		D36 Y75 F112 I122 D220
Annotation score1
Binding affinityMOAD: ic50=157uM
PDBbind-CN: -logKd/Ki=3.80,IC50=157uM
Enzymatic activity
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 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:3vv6, PDBe:3vv6, PDBj:3vv6
PDBsum3vv6
PubMed22998419
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]