Structure of PDB 5dqc Chain A Binding Site BS01

Receptor Information
>5dqc Chain A (length=372) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHD
EFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID5E7
InChIInChI=1S/C36H49N5O7S/c1-23(2)21-38-36(46)33(25(4)42)37-22-32(43)31(17-26-13-9-7-10-14-26)40-35(45)29-18-28(19-30(20-29)41(5)49(6,47)48)34(44)39-24(3)27-15-11-8-12-16-27/h7-16,18-20,23-25,31-33,37,42-43H,17,21-22H2,1-6H3,(H,38,46)(H,39,44)(H,40,45)/t24-,25+,31+,32-,33+/m1/s1
InChIKeyZIEVAMMZKBNDFB-AAZBAGLXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(C)CNC(=O)C(C(C)O)NCC(C(Cc1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)NC(C)c3ccccc3)O
CACTVS 3.385CC(C)CNC(=O)[CH](NC[CH](O)[CH](Cc1ccccc1)NC(=O)c2cc(cc(c2)C(=O)N[CH](C)c3ccccc3)N(C)[S](C)(=O)=O)[CH](C)O
ACDLabs 12.01CN(S(=O)(C)=O)c2cc(C(=O)NC(Cc1ccccc1)C(CNC(C(C)O)C(=O)NCC(C)C)O)cc(c2)C(=O)NC(C)c3ccccc3
OpenEye OEToolkits 1.9.2C[C@H](c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CN[C@@H]([C@H](C)O)C(=O)NCC(C)C)O
CACTVS 3.385CC(C)CNC(=O)[C@@H](NC[C@@H](O)[C@H](Cc1ccccc1)NC(=O)c2cc(cc(c2)C(=O)N[C@H](C)c3ccccc3)N(C)[S](C)(=O)=O)[C@H](C)O
FormulaC36 H49 N5 O7 S
NameN-[(2S,3R)-3-hydroxy-4-({(2S,3S)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
ChEMBL
DrugBank
ZINCZINC000219194105
PDB chain5dqc Chain A Residue 401 [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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PDB5dqc Design of Potent and Highly Selective Inhibitors for Human beta-Secretase 2 (Memapsin 1), a Target for Type 2 Diabetes.
Resolution2.4651 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 L30 D32 G34 S35 Y71 T72 Q73 F108 I118 Y198 D228 G230 T232 N233 R235
Binding residue
(residue number reindexed from 1)		G14 Q15 G16 L33 D35 G37 S38 Y74 T75 Q76 F111 I121 Y191 D221 G223 T225 N226 R228
Annotation score1
Binding affinityMOAD: Ki=45.6nM
PDBbind-CN: -logKd/Ki=7.34,Ki=45.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D221 T224
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:5dqc, PDBe:5dqc, PDBj:5dqc
PDBsum5dqc
PubMed27347366
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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