Structure of PDB 4w93 Chain A Binding Site BS02

Receptor Information
>4w93 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]
PYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVA
IYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVIN
HMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIEN
YNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASK
HMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGN
GRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHD
NQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQN
GNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNV
VDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYC
DVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Ligand information
Ligand ID3L9
InChIInChI=1S/C53H64O33/c1-15-31(62)37(68)42(73)50(77-15)81-28-14-76-49(41(72)35(28)66)83-45-23(59)8-18(9-24(45)60)44-46(36(67)30-22(58)10-19(55)11-25(30)79-44)84-52-47(39(70)32(63)16(2)78-52)86-53-48(85-51-43(74)38(69)33(64)26(12-54)80-51)40(71)34(65)27(82-53)13-75-29(61)6-4-17-3-5-20(56)21(57)7-17/h3-11,15-16,26-28,31-35,37-43,47-60,62-66,68-74H,12-14H2,1-2H3/b6-4+/t15-,16-,26+,27+,28+,31-,32-,33+,34+,35-,37+,38-,39+,40-,41+,42+,43+,47+,48+,49-,50-,51-,52-,53-/m0/s1
InChIKeyFHVDXUPJFGRQLV-OWPXYNISSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH]1O[CH](O[CH]2CO[CH](Oc3c(O)cc(cc3O)C4=C(O[CH]5O[CH](C)[CH](O)[CH](O)[CH]5O[CH]6O[CH](COC(=O)C=Cc7ccc(O)c(O)c7)[CH](O)[CH](O)[CH]6O[CH]8O[CH](CO)[CH](O)[CH](O)[CH]8O)C(=O)c9c(O)cc(O)cc9O4)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01O=C(OCC8OC(OC6C(O)C(O)C(OC6OC=1C(=O)c5c(O)cc(O)cc5OC=1c4cc(O)c(OC3OCC(OC2OC(C)C(O)C(O)C2O)C(O)C3O)c(O)c4)C)C(OC7OC(CO)C(O)C(O)C7O)C(O)C8O)\C=C\c9ccc(O)c(O)c9
CACTVS 3.385C[C@@H]1O[C@@H](O[C@@H]2CO[C@@H](Oc3c(O)cc(cc3O)C4=C(O[C@@H]5O[C@@H](C)[C@H](O)[C@@H](O)[C@H]5O[C@@H]6O[C@H](COC(=O)\C=C\c7ccc(O)c(O)c7)[C@@H](O)[C@H](O)[C@H]6O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8O)C(=O)c9c(O)cc(O)cc9O4)[C@H](O)[C@H]2O)[C@H](O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.9.2CC1C(C(C(C(O1)OC2COC(C(C2O)O)Oc3c(cc(cc3O)C4=C(C(=O)c5c(cc(cc5O4)O)O)OC6C(C(C(C(O6)C)O)O)OC7C(C(C(C(O7)COC(=O)C=Cc8ccc(c(c8)O)O)O)O)OC9C(C(C(C(O9)CO)O)O)O)O)O)O)O
OpenEye OEToolkits 1.9.2C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]2CO[C@H]([C@@H]([C@H]2O)O)Oc3c(cc(cc3O)C4=C(C(=O)c5c(cc(cc5O4)O)O)O[C@H]6[C@@H]([C@@H]([C@H]([C@@H](O6)C)O)O)O[C@H]7[C@@H]([C@H]([C@@H]([C@H](O7)COC(=O)/C=C/c8ccc(c(c8)O)O)O)O)O[C@H]9[C@@H]([C@H]([C@@H]([C@H](O9)CO)O)O)O)O)O)O)O
FormulaC53 H64 O33
NameMontbretin A;
2-(4-{[4-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-xylopyranosyl]oxy}-3,5-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl beta-D-glucopyranosyl-(1->2)-6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranosyl-(1->2)-6-deoxy-alpha-L-mannopyranoside
ChEMBL
DrugBank
ZINC
PDB chain4w93 Chain A Residue 503 [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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PDB4w93 The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif.
Resolution1.352 Å
Binding residue
(original residue number in PDB)
W58 W59 Y62 H101 Y151 L162 T163 L165 R195 D197 K200 H201 E233 I235 E240 D300
Binding residue
(residue number reindexed from 1)
W58 W59 Y62 H101 Y151 L162 T163 L165 R195 D197 K200 H201 E233 I235 E240 D300
Annotation score1
Binding affinityMOAD: Ki=8nM
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4w93, PDBe:4w93, PDBj:4w93
PDBsum4w93
PubMed26214255
UniProtP04746|AMYP_HUMAN Pancreatic alpha-amylase (Gene Name=AMY2A)

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