Structure of PDB 7zz9 Chain A Binding Site BS01

Receptor Information
>7zz9 Chain A (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
PLLKTTVKYGIKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGL
CMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFP
KHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFP
FWRRVHDSFIED
Ligand information
Ligand IDKG6
InChIInChI=1S/C28H35N13O9/c29-3-5-39(8-13-20(46)21(47)27(50-13)40-11-37-17-23(30)33-9-35-25(17)40)4-1-2-14-38-18-24(31)34-10-36-26(18)41(14)28-22(48)19(45)12(49-28)7-32-15(42)6-16(43)44/h9-13,19-22,27-28,45-48H,3-8,29H2,(H,32,42)(H,43,44)(H2,30,33,35)(H2,31,34,36)/t12-,13-,19-,20-,21-,22-,27-,28-/m1/s1
InChIKeySROHEFTVUSADJE-QJYUSYPVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCN(CC#Cc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CNC(=O)CC(O)=O)[C@@H](O)[C@H]3O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56
CACTVS 3.385NCCN(CC#Cc1nc2c(N)ncnc2n1[CH]3O[CH](CNC(=O)CC(O)=O)[CH](O)[CH]3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCN)CC#Cc4nc5c(ncnc5n4[C@H]6[C@@H]([C@@H]([C@H](O6)CNC(=O)CC(=O)O)O)O)N)O)O)N
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCN)CC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CNC(=O)CC(=O)O)O)O)N)O)O)N
FormulaC28 H35 N13 O9
Name3-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azanylethyl)amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-3-oxidanylidene-propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain7zz9 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]
PDB7zz9 Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		D45 G46 L49 F74 Y75 N122 E123 T161 A162 Y163 S166
Binding residue
(residue number reindexed from 1)		D45 G46 L49 F74 Y75 N120 E121 T159 A160 Y161 S164
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7zz9, PDBe:7zz9, PDBj:7zz9
PDBsum7zz9
PubMed36455355
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

[Back to BioLiP]