Structure of PDB 5idm Chain B Binding Site BS01

Receptor Information
>5idm Chain B (length=177) Species: 155892 (Caulobacter vibrioides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
REVLDLGELISEFEVLLRRLLREDVKLITDYGRDLPQVRADKSQLETAVM
NLAVNARDAVRAAKGGGVVRIRTARLTRDEAIQLGFPAADGDTAFIEVSD
DGPGIPPDVMGKIFDPFFTTKPVGEGTGLGLATVYGIVKQSDGWIHVHSR
PNEGAAFRIFLPVYEAPAALEHHHHHH
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 chain5idm Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5idm Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
E550 H551 H552 H553 H554 H555 H556
Binding residue
(residue number reindexed from 1)
E171 H172 H173 H174 H175 H176 H177
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.13.3: histidine kinase.
Gene Ontology
Molecular Function
GO:0016772 transferase activity, transferring phosphorus-containing groups
Biological Process
GO:0016310 phosphorylation

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Molecular Function

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Biological Process
External links
PDB RCSB:5idm, PDBe:5idm, PDBj:5idm
PDBsum5idm
PubMed27652341
UniProtQ9X688

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