Structure of PDB 2b8l Chain A Binding Site BS01

Receptor Information
>2b8l 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]
RRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAP
HPFLHRYYQRQLSSTYRDLRKGVYVPYTQGAWAGELGTDLVSIPHGPNVT
VRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQT
HVPNLFSLQLCGAVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRV
EINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEK
FPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYL
RPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAV
SACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID5HA
InChIInChI=1S/C31H38N4O5S/c1-21(23-12-8-5-9-13-23)33-30(37)24-17-25(19-27(18-24)35(2)41(3,39)40)31(38)34-28(16-22-10-6-4-7-11-22)29(36)20-32-26-14-15-26/h4-13,17-19,21,26,28-29,32,36H,14-16,20H2,1-3H3,(H,33,37)(H,34,38)/t21-,28+,29-/m1/s1
InChIKeyVPNIQGRFZCTBEZ-SPTGULJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H](c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CNC4CC4)O
CACTVS 3.341C[CH](NC(=O)c1cc(cc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CNC3CC3)N(C)[S](C)(=O)=O)c4ccccc4
CACTVS 3.341C[C@@H](NC(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CNC3CC3)N(C)[S](C)(=O)=O)c4ccccc4
OpenEye OEToolkits 1.5.0CC(c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)NC(Cc3ccccc3)C(CNC4CC4)O
ACDLabs 10.04O=S(=O)(N(c2cc(cc(C(=O)NC(c1ccccc1)C)c2)C(=O)NC(C(O)CNC3CC3)Cc4ccccc4)C)C
FormulaC31 H38 N4 O5 S
NameN-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2-HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE
ChEMBLCHEMBL378225
DrugBank
ZINCZINC000014960423
PDB chain2b8l Chain A Residue 386 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2b8l Conformationally biased P3 amide replacements of beta-secretase inhibitors
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 L30 D32 G34 Y71 T72 Q73 F108 W115 I118 D228 G230 T232 N233 R235 A335
Binding residue
(residue number reindexed from 1)		G17 Q18 G19 L36 D38 G40 Y77 T78 Q79 F114 W121 I124 D222 G224 T226 N227 R229 A329
Annotation score1
Binding affinityMOAD: ic50=15nM
PDBbind-CN: -logKd/Ki=7.82,IC50=15nM
BindingDB: IC50=15nM,EC50=43nM,Ki=233nM
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 D222 T225
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2b8l, PDBe:2b8l, PDBj:2b8l
PDBsum2b8l
PubMed16263281
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]