Structure of PDB 8std Chain D Binding Site BS02

Receptor Information
>8std Chain D (length=204) Species: 220668 (Lactiplantibacillus plantarum WCFS1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGFPEVIYGAGKTATQIVGIVQALSQQLPILTTRLSAEKFAALQPALPTA
VYHATAQCMTVGEQPAPKTPGYIAVVTAGTADQPVAEEAAVTAETFGNRV
ERVYDVGVAGIHRLFAKLDVIRGARVVIVIAGMEGALASVVGGLVDKPVI
AVPTSVGYGTSFQGMTALLTMLNSCASGITVVNIDNGFGAAYSASMVNQM
ASWS
Ligand information
Ligand IDDND
InChIInChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,19-,20-/m1/s1
InChIKeySENPVEZBRZQVST-HISDBWNOSA-O
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(c5)C(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(c5)C(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
FormulaC21 H27 N6 O15 P2
NameNICOTINIC ACID ADENINE DINUCLEOTIDE;
DEAMIDO-NAD+
ChEMBL
DrugBankDB04099
ZINCZINC000008216447
PDB chain8std Chain D Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8std Structure of the LarB-Substrate Complex and Identification of a Reaction Intermediate during Nickel-Pincer Nucleotide Cofactor Biosynthesis.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		A124 G125 T126 A127 D128 V154 A177 G178 E180 G181 A182 L183 V202
Binding residue
(residue number reindexed from 1)		A78 G79 T80 A81 D82 V108 A131 G132 E134 G135 A136 L137 V156
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.143: pyridinium-3,5-biscarboxylic acid mononucleotide synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016787 hydrolase activity
Biological Process
GO:0006189 'de novo' IMP biosynthetic process
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8std, PDBe:8std, PDBj:8std
PDBsum8std
PubMed37831946
UniProtF9UST0|LARB_LACPL Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (Gene Name=larB)

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