Structure of PDB 3bay Chain A Binding Site BS01

Receptor Information
>3bay Chain A (length=496) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVA
IYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVIN
HMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIEN
YNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASK
HMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGN
GRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDSHD
NQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQN
GNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNV
VDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYC
DVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Ligand information
Ligand IDARE
InChIInChI=1S/C31H53NO23/c1-7-13(16(39)22(45)29(49-7)54-26-11(5-35)50-28(48)21(44)19(26)42)32-9-2-8(3-33)25(18(41)14(9)37)53-31-24(47)20(43)27(12(6-36)52-31)55-30-23(46)17(40)15(38)10(4-34)51-30/h2,7,9-48H,3-6H2,1H3/t7-,9+,10-,11-,12-,13-,14+,15-,16+,17+,18-,19-,20-,21-,22-,23-,24-,25-,26-,27-,28+,29-,30-,31-/m1/s1
InChIKeyJUCZMZWYUIRMPL-NPPSNIQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](O)O[CH]2CO)[CH](O)[CH](O)[CH]1N[CH]3C=C(CO)[CH](O[CH]4O[CH](CO)[CH](O[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O)[CH](O)[CH]4O)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)O)CO)O)O)NC3C=C(C(C(C3O)O)OC4C(C(C(C(O4)CO)OC5C(C(C(C(O5)CO)O)O)O)O)O)CO
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)N[C@H]3C=C([C@H]([C@@H]([C@H]3O)O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O[C@@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)O)O)CO
CACTVS 3.341C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1N[C@H]3C=C(CO)[C@@H](O[C@H]4O[C@H](CO)[C@@H](O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O
ACDLabs 10.04O(C3C(=CC(NC2C(OC(OC1C(O)C(O)C(O)OC1CO)C(O)C2O)C)C(O)C3O)CO)C5OC(C(OC4OC(CO)C(O)C(O)C4O)C(O)C5O)CO
FormulaC31 H53 N O23
NameACARBOSE DERIVED PENTASACCHARIDE;
4-O-(4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}HE XOPYRANOSYL)HEXOPYRANOSE
ChEMBL
DrugBankDB04453
ZINCZINC000263620623
PDB chain3bay Chain A Residue 500 [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]
PDB3bay Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity
Resolution1.99 Å
Binding residue
(original residue number in PDB)		W58 W59 Y62 Q63 H101 Y151 T163 L165 R195 D197 A198 K200 H201 E233 D300
Binding residue
(residue number reindexed from 1)		W58 W59 Y62 Q63 H101 Y151 T163 L165 R195 D197 A198 K200 H201 E233 D300
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D197
Catalytic site (residue number reindexed from 1) D197
Enzyme Commision number 3.2.1.1: alpha-amylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004556 alpha-amylase activity
GO:0005509 calcium ion binding
GO:0016160 amylase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0031404 chloride ion binding
GO:0043169 cation binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0016052 carbohydrate catabolic process
GO:0044245 polysaccharide digestion
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bay, PDBe:3bay, PDBj:3bay
PDBsum3bay
PubMed18284212
UniProtP04746|AMYP_HUMAN Pancreatic alpha-amylase (Gene Name=AMY2A)

[Back to BioLiP]