Structure of PDB 4r93 Chain A Binding Site BS01

Receptor Information
>4r93 Chain A (length=386) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRAR
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID779
InChIInChI=1S/C26H39N5O2/c1-31-23(32)26(30-24(31)27,16-15-19-9-4-2-5-10-19)18-20-11-8-14-22(17-20)29-25(33)28-21-12-6-3-7-13-21/h3,6-7,12-13,19-20,22H,2,4-5,8-11,14-18H2,1H3,(H2,27,30)(H2,28,29,33)/t20-,22+,26+/m0/s1
InChIKeyCVMRAJSOLFSMNH-UNIVCBNLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=N)(CCC2CCCCC2)CC3CCCC(C3)NC(=O)Nc4ccccc4
CACTVS 3.385CN1C(=N)N[C@](CCC2CCCCC2)(C[C@H]3CCC[C@H](C3)NC(=O)Nc4ccccc4)C1=O
ACDLabs 12.01O=C1N(C(=[N@H])NC1(CC3CCCC(NC(=O)Nc2ccccc2)C3)CCC4CCCCC4)C
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@](C(=O)N1C)(CCC2CCCCC2)C[C@H]3CCC[C@H](C3)NC(=O)Nc4ccccc4
CACTVS 3.385CN1C(=N)N[C](CCC2CCCCC2)(C[CH]3CCC[CH](C3)NC(=O)Nc4ccccc4)C1=O
FormulaC26 H39 N5 O2
Name1-[(1R,3S)-3-{[(2E,4R)-4-(2-cyclohexylethyl)-2-imino-1-methyl-5-oxoimidazolidin-4-yl]methyl}cyclohexyl]-3-phenylurea
ChEMBLCHEMBL3354255
DrugBank
ZINCZINC000140718929
PDB chain4r93 Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r93 Discovery of potent iminoheterocycle BACE1 inhibitors.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		D93 Y132 K168 F169 I171 D289 G291
Binding residue
(residue number reindexed from 1)		D36 Y75 K111 F112 I114 D232 G234
Annotation score1
Binding affinityMOAD: Ki=16nM
PDBbind-CN: -logKd/Ki=7.80,Ki=16nM
BindingDB: Ki=16nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D232 T235
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:4r93, PDBe:4r93, PDBj:4r93
PDBsum4r93
PubMed25455483
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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