Structure of PDB 5qjb Chain D Binding Site BS01

Receptor Information
>5qjb Chain D (length=189) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTADGVAVIPVL
QRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETG
YKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDENARPKPKPGDGEFVE
VISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand IDK07
InChIInChI=1S/C10H14ClN3O/c1-14(5-8-2-3-15-6-8)10-9(11)4-12-7-13-10/h4,7-8H,2-3,5-6H2,1H3/t8-/m1/s1
InChIKeyOYKZBUOZAYBEHE-MRVPVSSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(CC1CCOC1)c2c(cncn2)Cl
CACTVS 3.385CN(C[C@H]1CCOC1)c2ncncc2Cl
ACDLabs 12.01n2c(N(CC1COCC1)C)c(cnc2)Cl
OpenEye OEToolkits 2.0.6CN(C[C@H]1CCOC1)c2c(cncn2)Cl
CACTVS 3.385CN(C[CH]1CCOC1)c2ncncc2Cl
FormulaC10 H14 Cl N3 O
Name5-chloro-N-methyl-N-{[(3R)-oxolan-3-yl]methyl}pyrimidin-4-amine
ChEMBL
DrugBank
ZINCZINC000097166125
PDB chain5qjb 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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PDB5qjb PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Resolution1.66 Å
Binding residue
(original residue number in PDB)		W46 E47
Binding residue
(residue number reindexed from 1)		W33 E34
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:5qjb, PDBe:5qjb, PDBj:5qjb
PDBsum5qjb
PubMed
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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