Structure of PDB 2hvd Chain B Binding Site BS01

Receptor Information
>2hvd Chain B (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 IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
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)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2hvd Chain B Residue 160 [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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PDB2hvd Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP
Resolution2.15 Å
Binding residue
(original residue number in PDB)		K12 L55 F60 L64 R88 T94 V112 N115
Binding residue
(residue number reindexed from 1)		K11 L54 F59 L63 R87 T93 V111 N114
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K12 Y52 N115 H118 E129
Catalytic site (residue number reindexed from 1) K11 Y51 N114 H117 E128
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:2hvd, PDBe:2hvd, PDBj:2hvd
PDBsum2hvd
PubMed16944299
UniProtP15531|NDKA_HUMAN Nucleoside diphosphate kinase A (Gene Name=NME1)

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