Structure of PDB 6qrl Chain B Binding Site BS01

Receptor Information
>6qrl Chain B (length=117) Species: 190650 (Caulobacter vibrioides CB15) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAPLEGRNVAIASPNAIVRAATARQIEAAGGRAYAAVDIASALAGAPADA
VLLIDAALSGPRGALKPPAGRRSVVLLTPEQRDRIDRLKAAGFSGYLIKP
LRAASLVAQVLQAVTAD
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 chain6qrl Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6qrl Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation.
Resolution1.84 Å
Binding residue
(original residue number in PDB)
R324 G337 Y338 I340 P342 R344 S347 Q351
Binding residue
(residue number reindexed from 1)
R82 G95 Y96 I98 P100 R102 S105 Q109
Annotation score4
Binding affinityMOAD: Kd=1.5uM
Enzymatic activity
Enzyme Commision number 2.7.13.3: histidine kinase.
Gene Ontology
Biological Process
GO:0000160 phosphorelay signal transduction system

View graph for
Biological Process
External links
PDB RCSB:6qrl, PDBe:6qrl, PDBj:6qrl
PDBsum6qrl
PubMed31882446
UniProtQ9ABT2

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