Structure of PDB 5dhr Chain A Binding Site BS01

Receptor Information
>5dhr 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 ID5AJ
InChIInChI=1S/C21H23N11O4S/c22-18-15-19(26-9-25-18)32(20-17(35)16(34)12(36-20)7-27-31-23)21(30-15)37-8-14(33)24-6-5-13-28-10-3-1-2-4-11(10)29-13/h1-4,9,12,16-17,20,34-35H,5-8H2,(H,24,33)(H,28,29)(H2,22,25,26)/t12-,16-,17-,20-/m1/s1
InChIKeyQNDDYPVSXWRDOZ-QQRWZLOUSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1nc2c(c(n1)N)nc(n2C3OC(C/N=[N+]=[N-])C(O)C3O)SCC(NCCc5nc4ccccc4n5)=O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3C5C(C(C(O5)CN=[N+]=[N-])O)O)N
OpenEye OEToolkits 1.9.2c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CN=[N+]=[N-])O)O)N
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12
FormulaC21 H23 N11 O4 S
Name5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine
ChEMBLCHEMBL3883775
DrugBank
ZINCZINC000584904853
PDB chain5dhr Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dhr 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		N122 E123 Y163 S166 H223
Binding residue
(residue number reindexed from 1)		N121 E122 Y162 S165 H222
Annotation score1
Binding affinityMOAD: Ki=23uM
PDBbind-CN: -logKd/Ki=4.64,Ki=23uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dhr, PDBe:5dhr, PDBj:5dhr
PDBsum5dhr
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

[Back to BioLiP]