Structure of PDB 6g14 Chain A Binding Site BS01

Receptor Information
>6g14 Chain A (length=281) Species: 367830 (Staphylococcus aureus subsp. aureus USA300) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIQWYPGHMAKAKREVSEQLKKVDVVFELVDARIPYSSRNPMIDEVINQK
PRVVILNKKDMSNLNEMSKWEQFFIDKGYYPVSVDAKHGKNLKKVEAAAI
KATAEKFEREKAKGLKPRAIRAMIVGIPNVGKSTLINKLAKRSIGNKPGV
TKQQQWIKVGNALQLLDTPGILWPKFEDEEVGKKLSLTGAIKHLDEVAIY
GLNFLIQNDLARLKSHYNIEVPEDAEIIAWFDAIGKKRGLIRRGNEIDYE
AVIELIIYDIRNAKIGNYCFDIFKDMTEELA
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 chain6g14 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6g14 Structural basis for (p)ppGpp-mediated inhibition of the GTPase RbgA.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N58 K59 D61 M62 D86 K88 N130 G132 K133 S134 T135
Binding residue
(residue number reindexed from 1)		N57 K58 D60 M61 D85 K87 N129 G131 K132 S133 T134
Annotation score3
Binding affinityMOAD: Kd=3.26uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006412 translation
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6g14, PDBe:6g14, PDBj:6g14
PDBsum6g14
PubMed30366986
UniProtA0A0H2XK72

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