Structure of PDB 3wb4 Chain A Binding Site BS01

Receptor Information
>3wb4 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]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAAEKFPDGF
WLGEQLVCWQANIFPVISLYLMGEVTNQSFRITILPQQYLRPVCYKFAIS
QSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFV
TLDMEDCGYN
Ligand information
Ligand ID0B3
InChIInChI=1S/C14H19N3O/c1-14(9-8-11-6-4-3-5-7-11)10-12(18)17(2)13(15)16-14/h3-7H,8-10H2,1-2H3,(H2,15,16)/t14-/m1/s1
InChIKeyNHJCZSSEYRWDOJ-CQSZACIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@]1(CC(=O)N(C(=N1)N)C)CCc2ccccc2
ACDLabs 12.01O=C2N(C(=NC(CCc1ccccc1)(C2)C)N)C
CACTVS 3.370CN1C(=O)C[C](C)(CCc2ccccc2)N=C1N
CACTVS 3.370CN1C(=O)C[C@@](C)(CCc2ccccc2)N=C1N
OpenEye OEToolkits 1.7.6CC1(CC(=O)N(C(=N1)N)C)CCc2ccccc2
FormulaC14 H19 N3 O
Name(6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one
ChEMBLCHEMBL3040447
DrugBank
ZINCZINC000028827218
PDB chain3wb4 Chain A Residue 507 [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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PDB3wb4 Conformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations
Resolution2.25 Å
Binding residue
(original residue number in PDB)		L30 D32 Y71 D228
Binding residue
(residue number reindexed from 1)		L32 D34 Y73 D220
Annotation score1
Binding affinityMOAD: Kd=36.6uM
PDBbind-CN: -logKd/Ki=4.44,Kd=36.6uM
BindingDB: IC50=34000nM
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 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3wb4, PDBe:3wb4, PDBj:3wb4
PDBsum3wb4
PubMed24051074
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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