Structure of PDB 3ckr Chain A Binding Site BS01

Receptor Information
>3ckr Chain A (length=379) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAP
HPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVT
VRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQT
HVPNLFSLQLCGAGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVII
VRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASS
TEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVESQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVS
ACHVHDEFRTAAVEGPFVTLDMEDCGYNI
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 A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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 Q73 F108 I110 R128 Y198 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		Q18 G19 D38 G40 Y77 T78 Q79 F114 I116 R134 Y195 D225 G227 T228 T229
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.30,Ki=5.001uM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D38 S41 N43 A45 Y77 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:3ckr, PDBe:3ckr, PDBj:3ckr
PDBsum3ckr
PubMed18434152
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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