Structure of PDB 1xd1 Chain A Binding Site BS01

Receptor Information
>1xd1 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
GRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHD
NQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQN
GNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNV
VDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYC
DVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Ligand information
Ligand ID6SA
InChIInChI=1S/C37H63NO28/c1-8-15(19(46)26(53)35(59-8)65-31-12(5-41)62-34(28(55)23(31)50)58-7-14-18(45)20(47)25(52)33(57)60-14)38-10-2-9(3-39)30(22(49)16(10)43)64-37-29(56)24(51)32(13(6-42)63-37)66-36-27(54)21(48)17(44)11(4-40)61-36/h2,8,10-57H,3-7H2,1H3/t8-,10+,11-,12-,13-,14-,15-,16+,17-,18-,19+,20+,21+,22-,23-,24-,25-,26-,27-,28-,29-,30-,31-,32-,33-,34+,35-,36-,37-/m1/s1
InChIKeyMBNITLCAVXHYER-DHAMQIFDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](OC[C@H]3O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]3O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1N[C@H]4C=C(CO)[C@@H](O[C@H]5O[C@H](CO)[C@@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OCC3C(C(C(C(O3)O)O)O)O)CO)O)O)NC4C=C(C(C(C4O)O)OC5C(C(C(C(O5)CO)OC6C(C(C(C(O6)CO)O)O)O)O)O)CO
CACTVS 3.341C[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](OC[CH]3O[CH](O)[CH](O)[CH](O)[CH]3O)O[CH]2CO)[CH](O)[CH](O)[CH]1N[CH]4C=C(CO)[CH](O[CH]5O[CH](CO)[CH](O[CH]6O[CH](CO)[CH](O)[CH](O)[CH]6O)[CH](O)[CH]5O)[CH](O)[CH]4O
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)OC[C@@H]3[C@H]([C@@H]([C@H]([C@@H](O3)O)O)O)O)CO)O)O)N[C@H]4C=C([C@H]([C@@H]([C@H]4O)O)O[C@@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O[C@@H]6[C@@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O)O)O)CO
ACDLabs 10.04O(C4C(=CC(NC3C(OC(OC2C(O)C(O)C(OCC1OC(O)C(O)C(O)C1O)OC2CO)C(O)C3O)C)C(O)C4O)CO)C6OC(C(OC5OC(CO)C(O)C(O)C5O)C(O)C6O)CO
FormulaC37 H63 N O28
NameACARBOSE DERIVED HEXASACCHARIDE;
4,6-DIDEOXY-4-{[(4R,5R)-4-[(4-O-ALPHA-D-ERYTHRO-HEXOPYRANOSYL-ALPHA-D-ERYTHRO-HEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)-ALPHA-D-XYLO-HEXOPYRANOSYL-(1->6)-BETA-D-ARABINO-HEXOPYRANOSE
ChEMBL
DrugBankDB03971
ZINCZINC000263620734
PDB chain1xd1 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

[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]
PDB1xd1 Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human Pancreatic alpha-Amylase in Complex with Analogues and Their Elongated Counterparts
Resolution2.2 Å
Binding residue
(original residue number in PDB)
W58 W59 Y62 Q63 H101 T163 R195 D197 K200 H201 E233 I235 E240 H299 D300 G306 A307
Binding residue
(residue number reindexed from 1)
W58 W59 Y62 Q63 H101 T163 R195 D197 K200 H201 E233 I235 E240 H299 D300 G306 A307
Annotation score1
Binding affinityMOAD: Ki=0.012uM
BindingDB: Ki=12nM
Enzymatic activity
Catalytic site (original residue number in PDB) D197 S226 D300
Catalytic site (residue number reindexed from 1) D197 S226 D300
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:1xd1, PDBe:1xd1, PDBj:1xd1
PDBsum1xd1
PubMed15736945
UniProtP04746|AMYP_HUMAN Pancreatic alpha-amylase (Gene Name=AMY2A)

[Back to BioLiP]