Structure of PDB 5kdf Chain A Binding Site BS04

Receptor Information

>5kdf Chain A (length=161) Species: 83332 (Mycobacterium tuberculosis H37Rv)

AMQFDVTIEIPKGQRNKYEVDHETGRVRLDRYLYTPMAYPTDYGFIEDTL
GDDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGD
PRWDHVQDIGDVPAFELDAIKHFFVHYKDLEPGKFVKAADWVDRAEAEAE
VQRSVERFKAG

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 5kdf Chain A Residue 205

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kdf Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from Mycobacterium tuberculosis.
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): K16 R30 D89 Y126 K127
• Binding residue (residue number reindexed from 1): K17 R31 D90 Y127 K128
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.1.1: inorganic diphosphatase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004427 inorganic diphosphate phosphatase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006796 phosphate-containing compound metabolic process

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0044228 host cell surface

External links

• PDB: RCSB:5kdf, PDBe:5kdf, PDBj:5kdf
• PDBsum: 5kdf
• PubMed: 27622287
• UniProt: P9WI55|IPYR_MYCTU Inorganic pyrophosphatase (Gene Name=ppa)