Structure of PDB 8jk9 Chain A Binding Site BS03

Receptor Information

>8jk9 Chain A (length=195) Species: 170187 (Streptococcus pneumoniae TIGR4)

SYQDYINCSREALLEKMAELLPEKRLTHCLGVERAAMELAQRFGVDVEKA
SLAGLLHDYAKKLSDQEFLVLIDRYQLDPDLKNWGNNVWHGMVGIYKIQE
DLDLHDSEILRAIEIHTVGAGQMTDLDKVIYVADYIEHNRAFPGVDVARE
IASLSLNKAVAYETARTVEYLAHQGFPIYPQTLETYNAFVHYLKE

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 8jk9 Chain A Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jk9 Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): R26 H29 D59 K62 N88 H91 H117 T118 D135 R141 L172 P178 I179 Y180 T183
• Binding residue (residue number reindexed from 1): R25 H28 D58 K61 N87 H90 H116 T117 D134 R140 L171 P177 I178 Y179 T182
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 3.6.1.41: bis(5'-nucleosyl)-tetraphosphatase (symmetrical).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005515 protein binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:8jk9, PDBe:8jk9, PDBj:8jk9
• PDBsum: 8jk9
• PubMed: 38701795
• UniProt: A0A0H2URF8