Structure of PDB 5dhp Chain D Binding Site BS02

Receptor Information
>5dhp Chain D (length=250) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KYMITSKGDEKSDLLRLNMIAGYDDVEPEIVISIGGDGTFLSAFHQYEER
LDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVK
KEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAY
NKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVN
DKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE
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 D 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 H223
Binding residue
(residue number reindexed from 1)		N109 E110 A149 Y150 S153 H210
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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