Structure of PDB 2rde Chain A Binding Site BS01

Receptor Information
>2rde Chain A (length=224) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEM
PKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAF
LSIPNTMQVSQLRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITP
PLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFN
EEGRNNAKNLLAQLKFNGTKLTLN
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 chain2rde Chain A Residue 301 [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]
PDB2rde The structural basis of cyclic diguanylate signal transduction by PilZ domains.
Resolution1.92 Å
Binding residue
(original residue number in PDB)
L135 R136 K137 R140 D162 S164 G167 C168 R169 N208 G219 L220 E221
Binding residue
(residue number reindexed from 1)
L112 R113 K114 R117 D139 S141 G144 C145 R146 N185 G196 L197 E198
Annotation score4
Binding affinityMOAD: Kd=97.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) T48
Catalytic site (residue number reindexed from 1) T25
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0035438 cyclic-di-GMP binding
Cellular Component
GO:0009288 bacterial-type flagellum

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:2rde, PDBe:2rde, PDBj:2rde
PDBsum2rde
PubMed18034161
UniProtA0A0H3ADR8

[Back to BioLiP]