Structure of PDB 5dhp Chain B Binding Site BS01

Receptor Information
>5dhp Chain B (length=263) 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
PLLKTTVKYKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCM
STPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKH
HVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFW
RRVHDSFIEDLEH
Ligand information
Ligand ID5AQ
InChIInChI=1S/C20H24N6O5S/c21-17-14-18(24-10-23-17)26(19-16(30)15(29)12(8-27)31-19)20(25-14)32-9-13(28)22-7-6-11-4-2-1-3-5-11/h1-5,10,12,15-16,19,27,29-30H,6-9H2,(H,22,28)(H2,21,23,24)/t12-,15-,16-,19-/m1/s1
InChIKeyWAETXEWYOOCYCX-BGIGGGFGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4ccccc4)nc12
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CO)[CH](O)[CH]3O)c(SCC(=O)NCCc4ccccc4)nc12
ACDLabs 12.01c4nc3n(C1C(C(C(O1)CO)O)O)c(SCC(NCCc2ccccc2)=O)nc3c(n4)N
OpenEye OEToolkits 1.9.2c1ccc(cc1)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)CO)O)O)N
OpenEye OEToolkits 1.9.2c1ccc(cc1)CCNC(=O)CSc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)N
FormulaC20 H24 N6 O5 S
Name8-({2-oxo-2-[(2-phenylethyl)amino]ethyl}sulfanyl)adenosine
ChEMBLCHEMBL3884345
DrugBank
ZINCZINC000584904973
PDB chain5dhp Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dhp 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		N122 E123 A162 Y163 S166 D222 H223
Binding residue
(residue number reindexed from 1)		N118 E119 A158 Y159 S162 D218 H219
Annotation score1
Binding affinityMOAD: Ki=140uM
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:5dhp, PDBe:5dhp, PDBj:5dhp
PDBsum5dhp
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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