Structure of PDB 5dhu Chain B Binding Site BS02

Receptor Information
>5dhu Chain B (length=262) 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
PLLKTTVKYKEATYLALNESTVKSSGPFVVDVVINDIHFERFRGDGLCMS
TPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHH
VVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWR
RVHDSFIEDLEH
Ligand information
Ligand ID5A8
InChIInChI=1S/C22H24N10O4S/c23-19-16-20(28-10-27-19)32(21-18(35)17(34)14(36-21)8-29-31-24)22(30-16)37-9-15(33)25-6-5-11-7-26-13-4-2-1-3-12(11)13/h1-4,7,10,14,17-18,21,26,34-35H,5-6,8-9H2,(H,25,33)(H2,23,27,28)/t14-,17-,18-,21-/m1/s1
InChIKeyNZVSVIHQZMZCNV-HAXDFEGKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c5nc4n(C1C(C(O)C(O1)CN=[N+]=[N-])O)c(SCC(NCCc3c2c(cccc2)nc3)=O)nc4c(n5)N
OpenEye OEToolkits 1.9.2c1ccc2c(c1)c(c[nH]2)CCNC(=O)CSc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CN=[N+]=[N-])O)O)N
OpenEye OEToolkits 1.9.2c1ccc2c(c1)c(c[nH]2)CCNC(=O)CSc3nc4c(ncnc4n3C5C(C(C(O5)CN=[N+]=[N-])O)O)N
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4c[nH]c5ccccc45)nc12
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4c[nH]c5ccccc45)nc12
FormulaC22 H24 N10 O4 S
Name5'-azido-5'-deoxy-8-[(2-{[2-(1H-indol-3-yl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine
ChEMBLCHEMBL3883397
DrugBank
ZINCZINC000584904824
PDB chain5dhu Chain D Residue 301 [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]
PDB5dhu 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		G131 P132 R148 G149 D150 A185
Binding residue
(residue number reindexed from 1)		G126 P127 R143 G144 D145 A180
Annotation score1
Binding affinityMOAD: Ki=0.5uM
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:5dhu, PDBe:5dhu, PDBj:5dhu
PDBsum5dhu
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

[Back to BioLiP]