Structure of PDB 1vj7 Chain B Binding Site BS03

Receptor Information
>1vj7 Chain B (length=310) Species: 119602 (Streptococcus dysgalactiae subsp. equisimilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
INLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHP
IQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDG
VTKLGKVESKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAP
LAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKLVDDIVTKIKSYT
TEQGLFGDVYGRPKHIYSIYRKMRIFDLIAIRCVMETQSDVYAMVGYIHE
LWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEY
GVAWIKELVE
Ligand information
Ligand IDGPX
InChIInChI=1S/C10H14N5O13P3/c11-10-13-7-4(8(16)14-10)12-2-15(7)9-6-5(26-31(22,23)27-6)3(25-9)1-24-30(20,21)28-29(17,18)19/h2-3,5-6,9H,1H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t3-,5-,6-,9-/m1/s1
InChIKeyNGYWTCOGOZELRS-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@H]4O[P@@](O)(=O)O[C@@H]34
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@@](=O)(O4)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C4C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O4)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH]4O[P](O)(=O)O[CH]34
ACDLabs 10.04O=P3(OC4C(OC(n1c2N=C(N)NC(=O)c2nc1)C4O3)COP(=O)(O)OP(=O)(O)O)O
FormulaC10 H14 N5 O13 P3
NameGUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE
ChEMBL
DrugBankDB02836
ZINCZINC000016051591
PDB chain1vj7 Chain B Residue 1999 [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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PDB1vj7 Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R44 K45 S46 N148 T151 L155 K159
Binding residue
(residue number reindexed from 1)		R40 K41 S42 N125 T128 L132 K136
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.6.5: GTP diphosphokinase.
3.1.7.2: guanosine-3',5'-bis(diphosphate) 3'-diphosphatase.
Gene Ontology
Biological Process
GO:0015969 guanosine tetraphosphate metabolic process

View graph for
Biological Process
External links
PDB RCSB:1vj7, PDBe:1vj7, PDBj:1vj7
PDBsum1vj7
PubMed15066282
UniProtQ54089|RELA_STREQ Bifunctional (p)ppGpp synthase/hydrolase RelA (Gene Name=relA)

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