Structure of PDB 7v2b Chain D Binding Site BS01

Receptor Information
>7v2b Chain D (length=376) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDSVPGSLVVVGGTYEPWLPVLEKVGWRCTQVADLRKPDALFVETGPCIG
IVDLSHDEFSLNGIANLVSSHKQVRWLAFIREAQLSSDTICQFIVNFCID
FFTAPIPDAQLLSTIGHQLGMLKLEKKVWPHFGSAGNMGLIGESMPMKRL
RDQIKRIGPTDVSILIYGESGTGKETVAKAIHKTSSRAQKPFISVNCRAM
SEKRLESELFGLGETEEGQQPFLLQADGGTLLLNDILTLPKSQQLNLLRF
LQEGTVETRQGVRAVDVRILAANSSDIEKALIDGDFNEELYHYINVLRIN
VPSLKERASDIVLLAKHFLQEYSKEYNAQARSFSDDAVRGLTRYHWPGNV
RELMNQIKRVVLMSDTVVLDESQLDL
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain7v2b Chain D Residue 501 [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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PDB7v2b Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G177 T178 G179 K180 E181 K185 M360
Binding residue
(residue number reindexed from 1)		G171 T172 G173 K174 E175 K179 M354
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008134 transcription factor binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

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Molecular Function
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Biological Process
External links
PDB RCSB:7v2b, PDBe:7v2b, PDBj:7v2b
PDBsum7v2b
PubMed34774564
UniProtQ9KU59

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