Structure of PDB 7u3d Chain A Binding Site BS04

Receptor Information
>7u3d Chain A (length=693) 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
TLLRFTRSMVRLRREHPVFRRRRFFHGRPVLTDIAWFTPEGEEMTSRDWQ
AAHAQALTVFLNGNAISEPGTQGERIADDSFLLMFNASAKELEFVVPDSH
GRYWRMVVDTSDPEGMPPQQGPELAGGERVTLAPLSLTVLRRP
Ligand information
Ligand IDC2E
InChIInChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKeyPKFDLKSEZWEFGL-MHARETSRSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(OC4C(OC(n2c3N=C(N)NC(=O)c3nc2)C4O)COP(=O)(O)OC5C6O)O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7C(=O)NC(=Nc67)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@H]3O)n6cnc7C(=O)NC(=Nc67)N
FormulaC20 H24 N10 O14 P2
Name9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one);
c-di-GMP;
Cyclic diguanosine monophosphate
ChEMBLCHEMBL1231573
DrugBank
ZINCZINC000072319544
PDB chain7u3d Chain A Residue 801 [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]
PDB7u3d Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
R31 E47 R49 T51 R56
Binding residue
(residue number reindexed from 1)
R30 E46 R48 T50 R55
Annotation score4
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:7u3d, PDBe:7u3d, PDBj:7u3d
PDBsum7u3d
PubMed36192422
UniProtA0A5P2ALW6

[Back to BioLiP]