Structure of PDB 3in3 Chain A Binding Site BS01

Receptor Information
>3in3 Chain A (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGFVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVII
VRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASS
TEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDCGY
Ligand information
Ligand ID472
InChIInChI=1S/C20H17N5O/c1-25-18(26)20(24-19(25)21,16-7-10-22-11-8-16)17-6-2-4-14(12-17)15-5-3-9-23-13-15/h2-13H,1H3,(H2,21,24)/t20-/m1/s1
InChIKeyAIKOTXHNUIYVMD-HXUWFJFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CN1C(=N[C](c2ccncc2)(c3cccc(c3)c4cccnc4)C1=O)N
ACDLabs 11.02O=C2N(C(=NC2(c1ccncc1)c4cccc(c3cccnc3)c4)N)C
CACTVS 3.352CN1C(=N[C@](c2ccncc2)(c3cccc(c3)c4cccnc4)C1=O)N
OpenEye OEToolkits 1.7.0CN1C(=O)C(N=C1N)(c2ccncc2)c3cccc(c3)c4cccnc4
OpenEye OEToolkits 1.7.0CN1C(=O)[C@@](N=C1N)(c2ccncc2)c3cccc(c3)c4cccnc4
FormulaC20 H17 N5 O
Name(5S)-2-amino-3-methyl-5-pyridin-4-yl-5-(3-pyridin-3-ylphenyl)-3,5-dihydro-4H-imidazol-4-one
ChEMBL
DrugBank
ZINCZINC000034804867
PDB chain3in3 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3in3 Di-substituted pyridinyl aminohydantoins as potent and highly selective human beta-secretase (BACE1) inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G73 G75 D94 S97 F170 I172 I180 D290 G292
Binding residue
(residue number reindexed from 1)		G14 G16 D35 S38 F111 I113 I121 D225 G227
Annotation score1
Binding affinityMOAD: ic50=0.06uM
PDBbind-CN: -logKd/Ki=7.22,IC50=0.06uM
BindingDB: IC50=60nM
Enzymatic activity
Catalytic site (original residue number in PDB) D94 S97 N99 A101 Y133 D290 T293
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D225 T228
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:3in3, PDBe:3in3, PDBj:3in3
PDBsum3in3
PubMed20045648
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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