Structure of PDB 5dht Chain A Binding Site BS02

Receptor Information
>5dht Chain A (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
PLLKTTVKYGIKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDG
LCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVF
PKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSF
PFWRRVHDSFIED
Ligand information
Ligand ID5A9
InChIInChI=1S/C20H22BrN9O4S/c21-11-3-1-2-10(6-11)4-5-24-13(31)8-35-20-28-14-17(22)25-9-26-18(14)30(20)19-16(33)15(32)12(34-19)7-27-29-23/h1-3,6,9,12,15-16,19,32-33H,4-5,7-8H2,(H,24,31)(H2,22,25,26)/t12-,15-,16-,19-/m1/s1
InChIKeyJYGMOYIMZQWVHO-BGIGGGFGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12
OpenEye OEToolkits 1.9.2c1cc(cc(c1)Br)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(Br)c4)nc12
OpenEye OEToolkits 1.9.2c1cc(cc(c1)Br)CCNC(=O)CSc2nc3c(ncnc3n2C4C(C(C(O4)CN=[N+]=[N-])O)O)N
ACDLabs 12.01c13c(c(N)ncn1)nc(SCC(NCCc2cc(Br)ccc2)=O)n3C4OC(C(C4O)O)CN=[N+]=[N-]
FormulaC20 H22 Br N9 O4 S
Name5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine
ChEMBLCHEMBL3884982
DrugBank
ZINCZINC000584904798
PDB chain5dht 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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PDB5dht 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		P132 G149 D150 A185
Binding residue
(residue number reindexed from 1)		P131 G148 D149 A184
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.00,Ki=1uM
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:5dht, PDBe:5dht, PDBj:5dht
PDBsum5dht
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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