Structure of PDB 5qj5 Chain C Binding Site BS03

Receptor Information
>5qj5 Chain C (length=192) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKQTADGVAVI
PVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEE
ETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDG
EFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHA
Ligand information
Ligand IDK0G
InChIInChI=1S/C12H11N3O/c16-12(14-10-5-2-1-3-6-10)15-11-7-4-8-13-9-11/h1-9H,(H2,14,15,16)
InChIKeyWBKYYDBHEGTTON-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(Nc1ccccc1)Nc2cccnc2
OpenEye OEToolkits 2.0.6c1ccc(cc1)NC(=O)Nc2cccnc2
ACDLabs 12.01N(c1cccnc1)C(Nc2ccccc2)=O
FormulaC12 H11 N3 O
NameN-phenyl-N'-pyridin-3-ylurea
ChEMBLCHEMBL1412642
DrugBank
ZINCZINC000000037406
PDB chain5qj5 Chain C Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5qj5 PanDDA analysis group deposition
Resolution1.72 Å
Binding residue
(original residue number in PDB)		R51 C139 I141
Binding residue
(residue number reindexed from 1)		R37 C124 I126
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.96: ADP-D-ribose pyrophosphorylase.
3.6.1.13: ADP-ribose diphosphatase.
3.6.1.58: 8-oxo-dGDP phosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0016787 hydrolase activity
GO:0017110 nucleoside diphosphate phosphatase activity
GO:0019144 ADP-sugar diphosphatase activity
GO:0030515 snoRNA binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044715 8-oxo-dGDP phosphatase activity
GO:0044716 8-oxo-GDP phosphatase activity
GO:0046872 metal ion binding
GO:0047631 ADP-ribose diphosphatase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006338 chromatin remodeling
GO:0006753 nucleoside phosphate metabolic process
GO:0009117 nucleotide metabolic process
GO:0009191 ribonucleoside diphosphate catabolic process
GO:0019303 D-ribose catabolic process
GO:0019693 ribose phosphate metabolic process
GO:0055086 nucleobase-containing small molecule metabolic process
GO:1990966 ATP generation from poly-ADP-D-ribose
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5qj5, PDBe:5qj5, PDBj:5qj5
PDBsum5qj5
PubMed
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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