Structure of PDB 5dhs Chain D Binding Site BS02

Receptor Information
>5dhs Chain D (length=245) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KYMITSKGDEKSDLLRLNMIAGYDDVEPEIVISIGGDGTFLSAFHQYEER
LDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKVSYPLLKTTVKKEATY
LALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLG
GALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQ
ISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE
Ligand information
Ligand ID5AG
InChIInChI=1S/C22H23N9O4S/c1-2-12-4-3-5-13(8-12)6-7-25-15(32)10-36-22-29-16-19(23)26-11-27-20(16)31(22)21-18(34)17(33)14(35-21)9-28-30-24/h1,3-5,8,11,14,17-18,21,33-34H,6-7,9-10H2,(H,25,32)(H2,23,26,27)/t14-,17-,18-,21-/m1/s1
InChIKeyHEZMFPGXYOAFRQ-HAXDFEGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C#Cc1cccc(c1)CCNC(=O)CSc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H]([C@H](O4)CN=[N+]=[N-])O)O)N
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4cccc(c4)C#C)nc12
OpenEye OEToolkits 1.9.2C#Cc1cccc(c1)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)CN=[N+]=[N-])O)O)N
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4cccc(c4)C#C)nc12
ACDLabs 12.01c4nc3n(C1C(C(O)C(O1)CN=[N+]=[N-])O)c(SCC(NCCc2cc(C#C)ccc2)=O)nc3c(n4)N
FormulaC22 H23 N9 O4 S
Name5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine
ChEMBLCHEMBL3883576
DrugBank
ZINCZINC000584904780
PDB chain5dhs Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dhs 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.62 Å
Binding residue
(original residue number in PDB)		N122 E123 A162 Y163
Binding residue
(residue number reindexed from 1)		N104 E105 A144 Y145
Annotation score1
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:5dhs, PDBe:5dhs, PDBj:5dhs
PDBsum5dhs
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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