Structure of PDB 5y6g Chain A Binding Site BS02

Receptor Information
>5y6g Chain A (length=131) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRRRYFRISAPLHPPYFCQTKLADNSTLRFRLYDLSLGGMGALLETAKPA
ELQEGMRFAQIEVNMGQWGVFHFDAQLISISERKVIDGKNETITTPRLSF
RFLNVSPTVERQLQRIIFSLEREAREKADKV
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 chain5y6g Chain A Residue 302 [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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PDB5y6g Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility inEscherichia coli.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
R113 R114 R115 R118 D145 G149 G150 M151 G152 R208 S210 F211 R212
Binding residue
(residue number reindexed from 1)
R2 R3 R4 R7 D34 G38 G39 M40 G41 R97 S99 F100 R101
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=7.00,Kd=99nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0035438 cyclic-di-GMP binding

View graph for
Molecular Function
External links
PDB RCSB:5y6g, PDBe:5y6g, PDBj:5y6g
PDBsum5y6g
PubMed31836667
UniProtP76010|YCGR_ECOLI Flagellar brake protein YcgR (Gene Name=ycgR)

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