Structure of PDB 7lnu Chain A Binding Site BS04

Receptor Information

>7lnu Chain A (length=239) Species: 1291540 (Methanomethylophilus alvi)

SHMILIKLGGSVITDKSEYHKFNKETVSRLADEIRRSGQDVMVVHGAGSF
GHVIAKKYAIQDGHVDDGQIPAAARIMCDTRELSSMVVEELLAQGIPAVS
VAPGSCFVMEDGKLIVDNEEPIRRLADLGIMPVMFGDVVPDRKKGFAIVS
GDQCMEVLCRMFDPEKVVFVSDIDGLYTADPKTDKKARLIGEVTSKMEAM
LRMTDRNRRCYLVNGNAPNRLYSLLKGETVTCTVAKGGM

Ligand information

• Ligand ID: IPE
• InChI: InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
• InChIKey: NUHSROFQTUXZQQ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: CC(=C)CCO[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: CC(=C)CCOP(=O)(O)OP(=O)(O)O
  ACDLabs 10.04: O=P(OP(=O)(O)O)(OCC\C(=C)C)O
  OpenEye OEToolkits 1.5.0: CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: CC(=C)CCO[P@](O)(=O)O[P](O)(O)=O
• Formula: C5 H12 O7 P2
• Name: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE;
  ISOPENTENYL PYROPHOSPHATE
• ChEMBL: CHEMBL356362
• DrugBank: DB04714
• ZINC: ZINC000008215654
• PDB chain: 7lnu Chain A Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lnu Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus .
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): A45 G49 H50 G134 I146 G149
• Binding residue (residue number reindexed from 1): A47 G51 H52 G136 I148 G151
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.7.4.26: isopentenyl phosphate kinase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0102043 isopentenyl phosphate kinase activity

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7lnu, PDBe:7lnu, PDBj:7lnu
• PDBsum: 7lnu
• PubMed: 34905349
• UniProt: M9SEQ1