Structure of PDB 7ztk Chain D Binding Site BS01

Receptor Information
>7ztk Chain D (length=152) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MANSERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFLQASEDLLKE
HYTDLKDRPFFTGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSK
PGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFQPEELVEYKSCAQNWI
YE
Ligand information
Ligand IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain7ztk Chain D 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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PDB7ztk Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K12 L55 F60 R88 T94 V112 N115 H118 D121 S122
Binding residue
(residue number reindexed from 1)		K12 L55 F60 R88 T94 V112 N115 H118 D121 S122
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004536 DNA nuclease activity
GO:0004550 nucleoside diphosphate kinase activity
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:0006231 dTMP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006259 DNA metabolic process
GO:0006897 endocytosis
GO:0007399 nervous system development
GO:0007595 lactation
GO:0009117 nucleotide metabolic process
GO:0016310 phosphorylation
GO:0030154 cell differentiation
GO:0030879 mammary gland development
GO:0050679 positive regulation of epithelial cell proliferation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005769 early endosome
GO:0005829 cytosol
GO:0032587 ruffle membrane
GO:0043209 myelin sheath

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7ztk, PDBe:7ztk, PDBj:7ztk
PDBsum7ztk
PubMed37672589
UniProtP15532|NDKA_MOUSE Nucleoside diphosphate kinase A (Gene Name=Nme1)

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