Structure of PDB 3kyf Chain A Binding Site BS03

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 503 [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)		R127 D157 T161 G162 C163 K164 R200 H201 G214 V215 R216
Binding residue
(residue number reindexed from 1)		R120 D150 T154 G155 C156 K157 R193 H194 G207 V208 R209
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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