Structure of PDB 6b09 Chain A Binding Site BS01

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 A 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)
R20 H24 R50 G60 F61 E76 E136 I164 S166 Q170
Binding residue
(residue number reindexed from 1)
R16 H20 R46 G56 F57 E72 E132 I160 S162 Q166
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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