Structure of PDB 5dht Chain C Binding Site BS02

Receptor Information
>5dht 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 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)		N122 E123 A162 Y163 S166 H223
Binding residue
(residue number reindexed from 1)		N119 E120 A159 Y160 S163 H220
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:5dht, PDBe:5dht, PDBj:5dht
PDBsum5dht
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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