Structure of PDB 5deo Chain A Binding Site BS01

Receptor Information

>5deo Chain A (length=189) Species: 561007 (Mycobacteroides abscessus ATCC 19977)

ERRRLGVMGGTFDPIHNGHLVAASEVADRFALDEVIFVPTGQGRKVSPAE
HRYLMTVIATASNPRFTVSRADIDRGGATYTVDTLTDLRTAHPDADLYFI
TGADALASILSWENWEQLFTLAKFIGVSRPGYELSSDHIAHADGLSLVEV
PALAISSTDCRIRAGQARPIWYLVPDGVVQYVAKHRLYS

Ligand information

• Ligand ID: DND
• InChI: InChI=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
• InChIKey: SENPVEZBRZQVST-HISDBWNOSA-O
• SMILES:
  CACTVS 3.385: Nc1ncnc2n(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 1.7.6: c1cc(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 3.385: Nc1ncnc2n(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 1.7.6: c1cc(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
• Formula: C21 H27 N6 O15 P2
• Name: NICOTINIC ACID ADENINE DINUCLEOTIDE;
  DEAMIDO-NAD+
• DrugBank: DB04099
• ZINC: ZINC000008216447
• PDB chain: 5deo Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5deo Mycobacterium abscessus NadD in complex with nicotinic acid adenine dinucleotide
• Resolution: 2.22 Å
• Binding residue (original residue number in PDB): M11 G12 G13 T14 H22 T43 Y88 T89 T109 G110 D112 W120 R137
• Binding residue (residue number reindexed from 1): M8 G9 G10 T11 H19 T40 Y80 T81 T101 G102 D104 W112 R129
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.7.7.18: nicotinate-nucleotide adenylyltransferase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004515 nicotinate-nucleotide adenylyltransferase activity
• GO:0005524 ATP binding
• GO:0016779 nucleotidyltransferase activity
• GO:0070566 adenylyltransferase activity

Biological Process

• GO:0009058 biosynthetic process
• GO:0009165 nucleotide biosynthetic process
• GO:0009435 NAD biosynthetic process
• GO:0019363 pyridine nucleotide biosynthetic process

External links

• PDB: RCSB:5deo, PDBe:5deo, PDBj:5deo
• PDBsum: 5deo
• UniProt: B1MMZ4