Structure of PDB 3in4 Chain A Binding Site BS01

Receptor Information
>3in4 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 IDBX2
InChIInChI=1S/C23H24N6O/c1-4-19-10-18(11-20(5-2)27-19)23(21(30)29(3)22(24)28-23)17-8-6-7-15(9-17)16-12-25-14-26-13-16/h6-14H,4-5H2,1-3H3,(H2,24,28)/t23-/m0/s1
InChIKeyQQPRKWVAAAEILV-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CCc1cc(cc(CC)n1)[C@@]2(N=C(N)N(C)C2=O)c3cccc(c3)c4cncnc4
ACDLabs 11.02O=C2N(C(=NC2(c1cc(nc(c1)CC)CC)c4cccc(c3cncnc3)c4)N)C
OpenEye OEToolkits 1.7.0CCc1cc(cc(n1)CC)C2(C(=O)N(C(=N2)N)C)c3cccc(c3)c4cncnc4
OpenEye OEToolkits 1.7.0CCc1cc(cc(n1)CC)[C@]2(C(=O)N(C(=N2)N)C)c3cccc(c3)c4cncnc4
CACTVS 3.352CCc1cc(cc(CC)n1)[C]2(N=C(N)N(C)C2=O)c3cccc(c3)c4cncnc4
FormulaC23 H24 N6 O
Name(5S)-2-amino-5-(2,6-diethylpyridin-4-yl)-3-methyl-5-(3-pyrimidin-5-ylphenyl)-3,5-dihydro-4H-imidazol-4-one
ChEMBLCHEMBL590730
DrugBank
ZINCZINC000038798476
PDB chain3in4 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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PDB3in4 Di-substituted pyridinyl aminohydantoins as potent and highly selective human beta-secretase (BACE1) inhibitors.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G73 Q74 D94 G96 S97 W138 F170 I172 W177 I180 D290 G292
Binding residue
(residue number reindexed from 1)		G14 Q15 D35 G37 S38 W79 F111 I113 W118 I121 D225 G227
Annotation score1
Binding affinityMOAD: ic50=0.04uM
PDBbind-CN: -logKd/Ki=7.52,IC50=0.03uM
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:3in4, PDBe:3in4, PDBj:3in4
PDBsum3in4
PubMed20045648
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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