Structure of PDB 7u3b Chain E Binding Site BS01

Receptor Information
>7u3b Chain E (length=696) Species: 54571 (Streptomyces venezuelae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVWPGQAYPLGATYDGAGTNFAVFSEAAHRIELCLLHDDGSETAVELRET
DAFVRHAYLPGVMPGQRYGFRVHGPYAPERGLRCNAAKLLLDPYARAVSG
RVRWGEAVYGYPFGRPDARNDLDSAPDTMTSVVVNPYFDWGDDRRPRTEY
HHTVIYEAHVKGLTMLHPDLPEELRGTYAGLAHPSVIGHLRELGVTALEL
MPVHQFVNDHRLVDAGLSNYWGYNTIGFFAPHNAYASWGDRGQQVLEFKS
AVRALHQAGIEVILDVVYNHTAEGNHLGPTLSMRGLDNPSYYRLADDPRY
YMDTTGTGNSLLMRSPHVLQLIMDSLRYWVTEMHVDGFRFDLAATLARQF
HEVDRLSSFFDLVQQDPVVSQVKLIAEPWDVGEGGYQVGNFPPLWTEWNG
KYRDCVRDLWRGEPRTLAEFASRLTGSSDLYQDDGRRPLASVNFVTCHDG
FTLRDLVSYNEKRNEANGEGNRDGENYNRSWNCGEEGETEDVGITELRAR
QMRNFLATLMLSQGVPMLSHGDEFGRTQGGNNNAYCQDNEVSWVRWPKEA
EATLLRFTRSMVRLRREHPVFRRRRFFHGRPVLTDIAWFTPEGEEMTSRD
WQAAHAQALTVFLNGNAISEPGTQGERIADDSFLLMFNASAKELEFVVPD
SHGRYWRMVVDTSDPEGMPPQQGPELAGGERVTLAPLSLTVLRRPA
Ligand information
Ligand IDA16
InChIInChI=1S/C19H35NO13/c1-5-9(20-7-2-6(3-21)10(23)13(26)11(7)24)12(25)16(29)19(31-5)33-17-8(4-22)32-18(30)15(28)14(17)27/h5-30H,2-4H2,1H3/t5-,6-,7+,8-,9-,10-,11+,12+,13+,14-,15-,16-,17-,18-,19-/m1/s1
InChIKeyARPGGXAVVRZVTA-FCTHMPQMSA-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[CH](CO)[CH](O)[CH](O)[CH]3O
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]3CC([C@H]([C@@H]([C@H]3O)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@H](CO)[C@@H](O)[C@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)O)CO)O)O)NC3CC(C(C(C3O)O)O)CO
ACDLabs 10.04OC3C(OC2OC(C)C(NC1CC(CO)C(O)C(O)C1O)C(O)C2O)C(OC(O)C3O)CO
FormulaC19 H35 N O13
Name4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose
ChEMBL
DrugBank
ZINCZINC000064511976
PDB chain7u3b Chain E Residue 801 [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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PDB7u3b Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP.
Resolution3.6 Å
Binding residue
(original residue number in PDB)
W222 G307 D342 H449 E470 N534 Y536
Binding residue
(residue number reindexed from 1)
W221 G306 D341 H448 E469 N533 Y535
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004133 glycogen debranching enzyme activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005980 glycogen catabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7u3b, PDBe:7u3b, PDBj:7u3b
PDBsum7u3b
PubMed36192422
UniProtA0A5P2ALW6

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