Structure of PDB 3ckr Chain B Binding Site BS01

Receptor Information
>3ckr Chain B (length=377) 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
GFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPV
EDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSAC
HVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID009
InChIInChI=1S/C37H43N5O3/c1-41(2)32-20-12-19-31(21-32)24-38-25-34(43)33(22-28-13-6-3-7-14-28)39-35(44)37(23-29-15-8-4-9-16-29)27-42(36(45)40-37)26-30-17-10-5-11-18-30/h3-21,33-34,38,43H,22-27H2,1-2H3,(H,39,44)(H,40,45)/t33-,34+,37-/m0/s1
InChIKeyDCJGHBWTJFHQCR-UEHMVRIRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(C)c1cccc(c1)CNC[C@H]([C@H](Cc2ccccc2)NC(=O)[C@@]3(CN(C(=O)N3)Cc4ccccc4)Cc5ccccc5)O
OpenEye OEToolkits 1.5.0CN(C)c1cccc(c1)CNCC(C(Cc2ccccc2)NC(=O)C3(CN(C(=O)N3)Cc4ccccc4)Cc5ccccc5)O
CACTVS 3.341CN(C)c1cccc(CNC[C@@H](O)[C@H](Cc2ccccc2)NC(=O)[C@@]3(CN(Cc4ccccc4)C(=O)N3)Cc5ccccc5)c1
CACTVS 3.341CN(C)c1cccc(CNC[CH](O)[CH](Cc2ccccc2)NC(=O)[C]3(CN(Cc4ccccc4)C(=O)N3)Cc5ccccc5)c1
ACDLabs 10.04O=C4N(Cc1ccccc1)CC(C(=O)NC(Cc2ccccc2)C(O)CNCc3cccc(N(C)C)c3)(N4)Cc5ccccc5
FormulaC37 H43 N5 O3
Name(4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide
ChEMBLCHEMBL406317
DrugBank
ZINCZINC000029049068
PDB chain3ckr Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ckr Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Q12 G13 D32 G34 Y71 T72 F108 I110 G230 T231 R235
Binding residue
(residue number reindexed from 1)		Q14 G15 D34 G36 Y73 T74 F110 I112 G221 T222 R226
Annotation score1
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:3ckr, PDBe:3ckr, PDBj:3ckr
PDBsum3ckr
PubMed18434152
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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