Structure of PDB 3kyg Chain A Binding Site BS03

Receptor Information
>3kyg Chain A (length=227) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLL
VEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVP
MAFLSIPNTMQVSQRRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRF
ITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGL
EFNEEGRNNAKNLLAQLKFNGTKLTLN
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain3kyg Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kyg Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R140 D162 S164 G167 C168 R169 C207 N208 G219 L220
Binding residue
(residue number reindexed from 1)		R120 D142 S144 G147 C148 R149 C187 N188 G199 L200
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=7.46,Kd=34.3nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0035438 cyclic-di-GMP binding
Biological Process
GO:0008150 biological_process
Cellular Component
GO:0005575 cellular_component
GO:0009288 bacterial-type flagellum
GO:0009425 bacterial-type flagellum basal body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kyg, PDBe:3kyg, PDBj:3kyg
PDBsum3kyg
PubMed20226196
UniProtQ9KNC3|YCGRL_VIBCH Cyclic di-GMP binding protein VCA0042 (Gene Name=VC_A0042)

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