Structure of PDB 7u3b Chain I Binding Site BS02

Receptor Information
>7u3b Chain I (length=696) Species: 54571 (Streptomyces venezuelae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQVWPGQAYPLGATYDGAGTNFAVFSEAAHRIELCLLHDDGSETAVELRE
TDAFVRHAYLPGVMPGQRYGFRVHGPYAPERGLRCNAAKLLLDPYARAVS
GRVRWGEAVYGYPFGRPDARNDLDSAPDTMTSVVVNPYFDWGDDRRPRTE
YHHTVIYEAHVKGLTMLHPDLPEELRGTYAGLAHPSVIGHLRELGVTALE
LMPVHQFVNDHRLVDAGLSNYWGYNTIGFFAPHNAYASWGDRGQQVLEFK
SAVRALHQAGIEVILDVVYNHTAEGNHLGPTLSMRGLDNPSYYRLADDPR
YYMDTTGTGNSLLMRSPHVLQLIMDSLRYWVTEMHVDGFRFDLAATLARQ
FHEVDRLSSFFDLVQQDPVVSQVKLIAEPWDVGEGGYQVGNFPPLWTEWN
GKYRDCVRDLWRGEPRTLAEFASRLTGSSDLYQDDGRRPLASVNFVTCHD
GFTLRDLVSYNEKRNEANGEGNRDGENYNRSWNCGEEGETEDVGITELRA
RQMRNFLATLMLSQGVPMLSHGDEFGRTQGGNNNAYCQDNEVSWVRWPKE
AEATLLRFTRSMVRLRREHPVFRRRRFFHGRPVELTDIAWFTPEGEEMTS
RDWQAAHAQALTVFLNGNAISEPGTQGERIADDSFLLMFNASAKELEFVV
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 I 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)
R212 H271 T308 D342 H449 D450 E470 N534
Binding residue
(residue number reindexed from 1)
R212 H271 T308 D342 H449 D450 E470 N534
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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