Structure of PDB 3wb5 Chain A Binding Site BS01

Receptor Information
>3wb5 Chain A (length=361) 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
GQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPD
GFWLGEQLVCWQAGWNIFPVISLYLMGEVTNQSFRITILPQQYLRPYKFA
ISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDFRTAAVEGPF
VTLDMEDCGYN
Ligand information
Ligand ID0B4
InChIInChI=1S/C15H19N3O/c1-15(9-13(19)18(2)14(16)17-15)12-8-11(12)10-6-4-3-5-7-10/h3-7,11-12H,8-9H2,1-2H3,(H2,16,17)/t11-,12+,15-/m0/s1
InChIKeyYBXYDJCRBQOXMI-ZOWXZIJZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@]1(CC(=O)N(C(=N1)N)C)[C@@H]2C[C@H]2c3ccccc3
OpenEye OEToolkits 1.7.6CC1(CC(=O)N(C(=N1)N)C)C2CC2c3ccccc3
CACTVS 3.385CN1C(=O)C[C](C)(N=C1N)[CH]2C[CH]2c3ccccc3
CACTVS 3.385CN1C(=O)C[C@](C)(N=C1N)[C@@H]2C[C@H]2c3ccccc3
ACDLabs 12.01O=C3N(C(=NC(C2CC2c1ccccc1)(C3)C)N)C
FormulaC15 H19 N3 O
Name(6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one
ChEMBLCHEMBL3040534
DrugBank
ZINCZINC000095920555
PDB chain3wb5 Chain A Residue 507 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wb5 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
Resolution2.501 Å
Binding residue
(original residue number in PDB)		D32 Y71 F108 D228
Binding residue
(residue number reindexed from 1)		D34 Y73 F110 D219
Annotation score1
Binding affinityMOAD: Kd=26.8uM
PDBbind-CN: -logKd/Ki=4.57,Kd=26.8uM
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:3wb5, PDBe:3wb5, PDBj:3wb5
PDBsum3wb5
PubMed24051074
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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