Structure of PDB 5e0f Chain A Binding Site BS01

Receptor Information
>5e0f 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 ID5J7
InChIInChI=1S/C36H36O20/c1-12-25(44)30(49)34(56-35-31(50)29(48)27(46)22(54-35)11-51-23(43)5-3-13-2-4-16(38)17(39)6-13)36(52-12)55-33-28(47)24-18(40)9-15(37)10-21(24)53-32(33)14-7-19(41)26(45)20(42)8-14/h2-10,12,22,25,27,29-31,34-42,44-46,48-50H,11H2,1H3/b5-3+/t12-,22+,25-,27+,29-,30+,31+,34+,35-,36-/m0/s1
InChIKeyYHIHWLPOKDIYGF-ZLGVOOGTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)OC2=C(Oc3cc(cc(c3C2=O)O)O)c4cc(c(c(c4)O)O)O)O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)COC(=O)/C=C/c6ccc(c(c6)O)O)O)O)O)O)O
CACTVS 3.385C[CH]1O[CH](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4cc(O)c(O)c(O)c4)[CH](O[CH]5O[CH](COC(=O)C=Cc6ccc(O)c(O)c6)[CH](O)[CH](O)[CH]5O)[CH](O)[CH]1O
CACTVS 3.385C[C@@H]1O[C@@H](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4cc(O)c(O)c(O)c4)[C@H](O[C@@H]5O[C@H](COC(=O)\C=C\c6ccc(O)c(O)c6)[C@@H](O)[C@H](O)[C@H]5O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.9.2CC1C(C(C(C(O1)OC2=C(Oc3cc(cc(c3C2=O)O)O)c4cc(c(c(c4)O)O)O)OC5C(C(C(C(O5)COC(=O)C=Cc6ccc(c(c6)O)O)O)O)O)O)O
ACDLabs 12.01c1c(c(O)c(O)cc1C=3Oc2cc(O)cc(O)c2C(=O)C=3OC4OC(C)C(C(C4OC5OC(C(C(C5O)O)O)COC(\C=C\c6cc(O)c(O)cc6)=O)O)O)O
FormulaC36 H36 O20
Name5,7-dihydroxy-4-oxo-2-(3,4,5-trihydroxyphenyl)-4H-chromen-3-yl 6-deoxy-2-O-{6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranosyl}-alpha-L-mannopyranoside
ChEMBL
DrugBank
ZINCZINC000261188673
PDB chain5e0f 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]
PDB5e0f Human pancreatic alpha-amylase in complex with mini-montbretin A
Resolution1.4 Å
Binding residue
(original residue number in PDB)		W58 W59 Y62 H101 L162 T163 L165 R195 D197 H201 E233 I235 D300
Binding residue
(residue number reindexed from 1)		W58 W59 Y62 H101 L162 T163 L165 R195 D197 H201 E233 I235 D300
Annotation score1
Binding affinityBindingDB: Ki=93.3nM
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:5e0f, PDBe:5e0f, PDBj:5e0f
PDBsum5e0f
PubMed
UniProtP04746|AMYP_HUMAN Pancreatic alpha-amylase (Gene Name=AMY2A)

[Back to BioLiP]