Structure of PDB 8jkr Chain A Binding Site BS01

Receptor Information

>8jkr Chain A (length=193) Species: 170187 (Streptococcus pneumoniae TIGR4)

SYQDYINCSREALLEKMAELLPEKRLTHCLGVERAAMELAQRFGVDVEKA
SLAGLLHDYAKKLSDQEFLVLIDRYQLDPDLKNWGNNVWHGMVGIYKIQE
DLDLHDSEILRAIEIHTVGAGQMTDLDKVIYVADYIEHNRAFPGVDVARE
IASLSLNKAVAYETARTVEYLAHQGFPIYPQTLETYNAFVHYL

Ligand information

• Ligand ID: U5P
• InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: DJJCXFVJDGTHFX-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: URIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL214393
• DrugBank: DB03685
• ZINC: ZINC000002123545
• PDB chain: 8jkr Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jkr Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): N88 H91 H117 T118 D135 T168 L172 Y180 T183
• Binding residue (residue number reindexed from 1): N87 H90 H116 T117 D134 T167 L171 Y179 T182
• Annotation score: 2

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:8jkr, PDBe:8jkr, PDBj:8jkr
• PDBsum: 8jkr
• PubMed: 38701795
• UniProt: A0A0H2URF8