Structure of PDB 7zza Chain A Binding Site BS01

Receptor Information
>7zza Chain A (length=261) 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
PLLKTTVKYGKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLC
MSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPK
HHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPF
WRRVHDSFIED
Ligand information
Ligand IDKH9
InChIInChI=1S/C29H38N14O9/c30-4-2-5-33-29(50)34-7-13-19(46)22(49)28(51-13)43-15(40-18-24(32)36-11-38-26(18)43)3-1-6-41(9-16(44)45)8-14-20(47)21(48)27(52-14)42-12-39-17-23(31)35-10-37-25(17)42/h10-14,19-22,27-28,46-49H,2,4-9,30H2,(H,44,45)(H2,31,35,37)(H2,32,36,38)(H2,33,34,50)/t13-,14-,19-,20-,21-,22-,27-,28-/m1/s1
InChIKeyPFWXIFMXYVCTQE-CGZJSAOLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCCNC(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2c(nc3c(N)ncnc23)C#CCN(C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)CC(O)=O
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CNC(=O)NCCCN)O)O)N)CC(=O)O)O)O)N
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC#Cc4nc5c(ncnc5n4[C@H]6[C@@H]([C@@H]([C@H](O6)CNC(=O)NCCCN)O)O)N)CC(=O)O)O)O)N
CACTVS 3.385NCCCNC(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(nc3c(N)ncnc23)C#CCN(C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)CC(O)=O
FormulaC29 H38 N14 O9
Name2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(3-azanylpropylcarbamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid
ChEMBL
DrugBank
ZINC
PDB chain7zza Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7zza Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria.
Resolution2.05 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 N119 E120 T158 A159 Y160 S163
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:7zza, PDBe:7zza, PDBj:7zza
PDBsum7zza
PubMed36455355
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

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