Structure of PDB 8oov Chain C Binding Site BS01

Receptor Information
>8oov Chain C (length=151) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEH
YVDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKP
GTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIY
E
Ligand information
Ligand IDPAP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKeyGBBWIZKLHXYJOA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O
FormulaC10 H16 N5 O13 P3
Name3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB01842
ZINCZINC000013527438
PDB chain8oov Chain C Residue 201 [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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PDB8oov A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K12 Y52 L55 R58 F60 R88 T94 N115 H118
Binding residue
(residue number reindexed from 1)		K11 Y51 L54 R57 F59 R87 T93 N114 H117
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0004536 DNA nuclease activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0008408 3'-5' exonuclease activity
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0043024 ribosomal small subunit binding
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006259 DNA metabolic process
GO:0006897 endocytosis
GO:0007399 nervous system development
GO:0007595 lactation
GO:0008285 negative regulation of cell population proliferation
GO:0009117 nucleotide metabolic process
GO:0016310 phosphorylation
GO:0030154 cell differentiation
GO:0030879 mammary gland development
GO:0042981 regulation of apoptotic process
GO:0043388 positive regulation of DNA binding
GO:0050679 positive regulation of epithelial cell proliferation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005769 early endosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0032587 ruffle membrane
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:8oov, PDBe:8oov, PDBj:8oov
PDBsum8oov
PubMed37298313
UniProtP15531|NDKA_HUMAN Nucleoside diphosphate kinase A (Gene Name=NME1)

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