Structure of PDB 7pmz Chain D Binding Site BS02

Receptor Information
>7pmz Chain D (length=428) Species: 100226 (Streptomyces coelicolor A3(2)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVPEKFATLGLTYDDVLLLPGASAVLPNAVDTSSRISRNVRVNIPLLSAA
MDKVTESRMAISMARQGGVGVLHRNLSIEDQANQVDLVKRSESGMVANPI
TIHPDATLGEADALCAKFRISGVPVTDGAGKLLGIVTNRDMAFETDRSRQ
VREVMTPMPLVTGQVGISGVDAMELLRRHKIEKLPLVDGDGILKGLITVK
DFVKAEQYPHAAKDAKGRLLVGAAVGASPEALDRAQALAEAGVDFLVVDT
SHGHNSNALSWMSKIKSSVGIDVVGGNVATRDGAQALIDAGVDGIKVGVG
PGSICTTRVVAGIGVPQVTAIYEASLAARAAGVPLIGDGGLQYSGDIGKA
LAAGADTVMLGSLLAGCEESPGELQFINGKQFKVPYRGPLANVLHQLVGG
LRQTMGYVGAATIEEMESKGRFVRITSA
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 chain7pmz Chain D Residue 601 [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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PDB7pmz Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		R71 C121 A122 R125 I126 S127 N144 E188 K206 K210
Binding residue
(residue number reindexed from 1)		R65 C115 A116 R119 I120 S121 N138 E182 K200 K204
Annotation score2
Enzymatic activity
Enzyme Commision number 1.1.1.205: IMP dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0003938 IMP dehydrogenase activity
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006177 GMP biosynthetic process
GO:0006183 GTP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7pmz, PDBe:7pmz, PDBj:7pmz
PDBsum7pmz
PubMed35481629
UniProtQ9L0I7

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