Structure of PDB 5dhq Chain C Binding Site BS02

Receptor Information
>5dhq Chain C (length=260) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYMITSKGDEKSDLLRLNMIAGFGYDMEYDDVEPEIVISIGGDGTFLSA
FHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYP
LLKTTVKYGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLC
MSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPK
HHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPF
WRRVHDSFIE
Ligand information
Ligand ID5AK
InChIInChI=1S/C20H23BrN6O5S/c21-11-3-1-2-10(6-11)4-5-23-13(29)8-33-20-26-14-17(22)24-9-25-18(14)27(20)19-16(31)15(30)12(7-28)32-19/h1-3,6,9,12,15-16,19,28,30-31H,4-5,7-8H2,(H,23,29)(H2,22,24,25)/t12-,15-,16-,19-/m1/s1
InChIKeyWJGLUXUMEHFNOZ-BGIGGGFGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CO)[CH](O)[CH]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12
ACDLabs 12.01c31ncnc(c1nc(SCC(NCCc2cc(Br)ccc2)=O)n3C4C(C(C(O4)CO)O)O)N
OpenEye OEToolkits 1.9.2c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)CO)O)O)N
OpenEye OEToolkits 1.9.2c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)N
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12
FormulaC20 H23 Br N6 O5 S
Name8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine
ChEMBLCHEMBL3883980
DrugBank
ZINCZINC000584904984
PDB chain5dhq Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dhq 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		N122 E123 A162 Y163 S166 H223
Binding residue
(residue number reindexed from 1)		N119 E120 A159 Y160 S163 H220
Annotation score1
Binding affinityMOAD: Ki=2uM
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:5dhq, PDBe:5dhq, PDBj:5dhq
PDBsum5dhq
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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