Structure of PDB 5nwh Chain A Binding Site BS01

Receptor Information
>5nwh Chain A (length=193) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVA
VIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALREL
EEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKDG
EFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand ID9CH
InChIInChI=1S/C20H20Cl2N8O3/c1-27-16-15(18(31)28(2)20(27)32)30(19(24-16)29-7-5-23-6-8-29)10-14-25-26-17(33-14)11-3-4-12(21)13(22)9-11/h3-4,9,23H,5-8,10H2,1-2H3
InChIKeyQXCXMVYVUHVFLP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)N(C)c2nc(N3CCNCC3)n(Cc4oc(nn4)c5ccc(Cl)c(Cl)c5)c2C1=O
OpenEye OEToolkits 2.0.6CN1c2c(n(c(n2)N3CCNCC3)Cc4nnc(o4)c5ccc(c(c5)Cl)Cl)C(=O)N(C1=O)C
FormulaC20 H20 Cl2 N8 O3
Name7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione
ChEMBL
DrugBank
ZINC
PDB chain5nwh Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5nwh Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		W28 R51 R84 L98 I141
Binding residue
(residue number reindexed from 1)		W15 R38 R71 L85 I128
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.54,IC50=29nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nwh, PDBe:5nwh, PDBj:5nwh
PDBsum5nwh
PubMed29343827
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

[Back to BioLiP]