Structure of PDB 6rgc Chain A Binding Site BS01

Receptor Information
>6rgc Chain A (length=259) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLS
AFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSY
PLLKTTVKYEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMS
TPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHH
VVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWR
RVHDSFIED
Ligand information
Ligand IDK3H
InChIInChI=1S/C24H29N11O7/c1-33(5-10-15(37)17(39)23(41-10)34-9-31-13-19(25)27-7-29-21(13)34)4-2-3-12-32-14-20(26)28-8-30-22(14)35(12)24-18(40)16(38)11(6-36)42-24/h7-11,15-18,23-24,36-40H,4-6H2,1H3,(H2,25,27,29)(H2,26,28,30)/t10-,11-,15-,16-,17-,18-,23-,24-/m1/s1
InChIKeyOPWBYPZWGGCZGG-KRSQEUQLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN(CC#Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)C[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O
CACTVS 3.385CN(CC#Cc1nc2c(N)ncnc2n1[CH]3O[CH](CO)[CH](O)[CH]3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56
OpenEye OEToolkits 2.0.7CN(CC#Cc1nc2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)CC4C(C(C(O4)n5cnc6c5ncnc6N)O)O
CACTVS 3.385CN(CC#Cc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56
FormulaC24 H29 N11 O7
Name(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-methyl-amino]methyl]oxolane-3,4-diol
ChEMBL
DrugBank
ZINC
PDB chain6rgc Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rgc From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		D45 G46 L72 F74 N122 E123 T161 A162 Y163 S166
Binding residue
(residue number reindexed from 1)		D45 G46 L72 F74 N117 E118 T156 A157 Y158 S161
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.1.23: NAD(+) kinase.
Gene Ontology
Molecular Function
GO:0003951 NAD+ kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006741 NADP biosynthetic process
GO:0016310 phosphorylation
GO:0019674 NAD metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rgc, PDBe:6rgc, PDBj:6rgc
PDBsum6rgc
PubMed32017533
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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