Structure of PDB 6vwp Chain A Binding Site BS01

Receptor Information
>6vwp Chain A (length=435) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMKFPGKRKSKHYFPVNARDPLLQQFQPENETSAAWVVGIDQTLVDIEAK
VDDEFIERYGLSAGHSLVIEDDVAEALYQELKQKNLITHQFAGGTIGNTM
HNYSVLADDRSVLLGVMCSNIEIGSYAYRYLCNTSSRTDLNYLQGVDGPI
GRCFTLIGESGERTFAISPGHMNQLRAESIPEDVIAGASALVLTSYLVRC
KPGEPMPEATMKAIEYAKKYNVPVVLTLGTKFVIAENPQWWQQFLKDHVS
ILAMNEDEAEALTGESDPLLASDKALDWVDLVLCTAGPIGLYMAGFTEDE
AKRKTQHPLLPGAIAEFNQYEFSRAMRHKDCQNPLRVYSHIAPYMGGPEK
IMNTNGAGDGALAALLHDITANSYHRSNVPNSSKHKFTWLTYSSLAQVCK
YANRVSYQVLNQHSPRLTRGLPEREDSLEESYWDR
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain6vwp Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vwp ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		R7 S9 K10 H11 R302 F321 K383 S393 Q396
Binding residue
(residue number reindexed from 1)		R8 S10 K11 H12 R303 F322 K384 S394 Q397
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.1.73: inosine kinase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008906 inosine kinase activity
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0097216 guanosine tetraphosphate binding
GO:0106366 guanosine kinase activity
Biological Process
GO:0006166 purine ribonucleoside salvage
GO:0016310 phosphorylation
GO:0032263 GMP salvage
GO:0032264 IMP salvage

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vwp, PDBe:6vwp, PDBj:6vwp
PDBsum6vwp
PubMed32857952
UniProtP0AEW6|INGK_ECOLI Guanosine-inosine kinase (Gene Name=gsk)

[Back to BioLiP]