Structure of PDB 3kyf Chain A Binding Site BS04

Receptor Information
>3kyf Chain A (length=231) Species: 160488 (Pseudomonas putida KT2440) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESN
TLALDEMIPRDGEKFIENGEHFRVEGFHDGVRIAWECDHALKISEVDGHR
CYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLD
ISATGCKLRFEGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEER
INTTFAGVRFHNLSGQAQRKIESFVYQLQRE
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 chain3kyf Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kyf 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)		R122 R123 N124 R127
Binding residue
(residue number reindexed from 1)		R115 R116 N117 R120
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.78,Kd=165.0nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0035438 cyclic-di-GMP binding
Biological Process
GO:0071945 regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed
GO:0071973 bacterial-type flagellum-dependent cell motility
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:3kyf, PDBe:3kyf, PDBj:3kyf
PDBsum3kyf
PubMed20226196
UniProtQ88EQ6|YCGR_PSEPK Flagellar brake protein YcgR (Gene Name=ycgR)

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