Structure of PDB 7ody Chain A Binding Site BS05

Receptor Information

>7ody Chain A (length=99) Species: 260586 (Cyanophage S-2L)

PATVAELQAEIAAWIHPLNPDRRPGGTIAKLLEEIGELIASDRDPLEVAD
VLILALDLATLLGVDVTEAIRAKLAINRARSWARADNGAMRHIPGSDTP

Ligand information

• Ligand ID: DGI
• InChI: InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
• InChIKey: CIKGWCTVFSRMJU-KVQBGUIXSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O10 P2
• Name: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL1232205
• DrugBank: DB03491
• ZINC: ZINC000008215878
• PDB chain: 7ody Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ody Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA.
• Resolution: 1.43 Å
• Binding residue (original residue number in PDB): K76 R83 W85 A92 M93 R94 H95
• Binding residue (residue number reindexed from 1): K73 R80 W82 A89 M90 R91 H92
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.1.9: nucleotide diphosphatase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:7ody, PDBe:7ody, PDBj:7ody
• PDBsum: 7ody
• PubMed: 34354070
• UniProt: A0A7U3TBV3|DGTPH_BPS2L dATP/dGTP diphosphohydrolase (Gene Name=S2L_23)