Structure of PDB 8ptt Chain D Binding Site BS02

Receptor Information
>8ptt Chain D (length=195) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVA
VIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALREL
EEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPG
DGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand IDF2V
InChIInChI=1S/C20H20ClF3N6/c1-28-12-27-17-16(28)18(26-11-25-17)30-7-5-19(10-30)4-6-29(9-19)13-2-3-14(15(21)8-13)20(22,23)24/h2-3,8,11-12H,4-7,9-10H2,1H3/t19-/m1/s1
InChIKeyCAPZLSKZPWSIKV-LJQANCHMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cn1cnc2c1c(ncn2)N3CCC4(C3)CCN(C4)c5ccc(c(c5)Cl)C(F)(F)F
CACTVS 3.385Cn1cnc2ncnc(N3CC[C@@]4(CCN(C4)c5ccc(c(Cl)c5)C(F)(F)F)C3)c12
CACTVS 3.385Cn1cnc2ncnc(N3CC[C]4(CCN(C4)c5ccc(c(Cl)c5)C(F)(F)F)C3)c12
OpenEye OEToolkits 2.0.7Cn1cnc2c1c(ncn2)N3CC[C@]4(C3)CCN(C4)c5ccc(c(c5)Cl)C(F)(F)F
FormulaC20 H20 Cl F3 N6
Name6-[(5~{R})-7-[3-chloranyl-4-(trifluoromethyl)phenyl]-2,7-diazaspiro[4.4]nonan-2-yl]-7-methyl-purine
ChEMBL
DrugBank
ZINC
PDB chain8ptt Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ptt Human NUDT5 in complex with MRK-952
Resolution2.5 Å
Binding residue
(original residue number in PDB)		W28 A96 I141
Binding residue
(residue number reindexed from 1)		W15 A83 I128
Annotation score1
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:8ptt, PDBe:8ptt, PDBj:8ptt
PDBsum8ptt
PubMed
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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