Structure of PDB 6b09 Chain A Binding Site BS03

Receptor Information
>6b09 Chain A (length=176) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GARRLELGEALALGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGR
LGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGP
RVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGG
LPTFLENSFIGSAREQLLEALQDLGL
Ligand information
Ligand IDC7G
InChIInChI=1S/C25H36N10O23P4/c26-19-11-21(30-4-28-19)34(6-32-11)23-16(39)13(36)8(53-23)1-51-61(46,47)58-62(48,49)52-2-9-14(37)17(40)25(55-9)56-18-15(38)10(3-50-60(44,45)57-59(41,42)43)54-24(18)35-7-33-12-20(27)29-5-31-22(12)35/h4-10,13-18,23-25,36-40H,1-3H2,(H,44,45)(H,46,47)(H,48,49)(H2,26,28,30)(H2,27,29,31)(H2,41,42,43)/t8-,9+,10-,13+,14-,15+,16+,17+,18+,23+,24+,25+/m1/s1
InChIKeyCSEMRHUJDKFXPV-OATIKAJMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(cnc12)[C@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H]4O[C@@H](O[C@H]5[C@@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O[C@@H]5n6cnc7c(N)ncnc67)[C@@H](O)[C@@H]4O)[C@H](O)[C@@H]3O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@@H]3[C@H]([C@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H]4[C@H]([C@@H]([C@@H](O4)O[C@H]5[C@H]([C@H](O[C@@H]5n6cnc7c6ncnc7N)COP(=O)(O)OP(=O)(O)O)O)O)O)O)O)N
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)OC5C(C(OC5n6cnc7c6ncnc7N)COP(=O)(O)OP(=O)(O)O)O)O)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O[CH]5[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O[CH]5n6cnc7c(N)ncnc67)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC25 H36 N10 O23 P4
Name[(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate;
DIADPR
ChEMBL
DrugBank
ZINC
PDB chain6b09 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6b09 Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
R149 D150
Binding residue
(residue number reindexed from 1)
R145 D146
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.62: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
3.6.1.64: inosine diphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0008235 metalloexopeptidase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0030515 snoRNA binding
GO:0031404 chloride ion binding
GO:0035870 dITP diphosphatase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
GO:0097383 dIDP phosphatase activity
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
GO:1990003 IDP phosphatase activity
GO:1990174 phosphodiesterase decapping endonuclease activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0009117 nucleotide metabolic process
GO:0016077 sno(s)RNA catabolic process
GO:0035863 dITP catabolic process
GO:0090068 positive regulation of cell cycle process
GO:0110155 NAD-cap decapping
GO:2000233 negative regulation of rRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
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:6b09, PDBe:6b09, PDBj:6b09
PDBsum6b09
PubMed30976021
UniProtQ96DE0|NUD16_HUMAN U8 snoRNA-decapping enzyme (Gene Name=NUDT16)

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