Structure of PDB 8dkp Chain B Binding Site BS02

Receptor Information

>8dkp Chain B (length=388) Species: 707241 (Sinorhizobium meliloti SM11)

SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEA
LRGKHSMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADA
ERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQAARVMG
ELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWN
GMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQL
DGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYH
MAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLL
AYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVV

Ligand information

• Ligand ID: TFB
• InChI: InChI=1S/C5H8O3/c6-5(7)4-2-1-3-8-4/h4H,1-3H2,(H,6,7)/t4-/m0/s1
• InChIKey: UJJLJRQIPMGXEZ-BYPYZUCNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1CC(OC1)C(=O)O
  ACDLabs 10.04: O=C(O)C1OCCC1
  OpenEye OEToolkits 1.5.0: C1C[C@H](OC1)C(=O)O
  CACTVS 3.341: OC(=O)[C@@H]1CCCO1
  CACTVS 3.341: OC(=O)[CH]1CCCO1
• Formula: C5 H8 O3
• Name: TETRAHYDROFURAN-2-CARBOXYLIC ACID
• ZINC: ZINC000002164321
• PDB chain: 8dkp Chain B Residue 2002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dkp Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery.
• Resolution: 1.23 Å
• Binding residue (original residue number in PDB): K265 D306 Y473 R488 R489
• Binding residue (residue number reindexed from 1): K132 D173 Y340 R355 R356
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
  1.5.5.2: proline dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
• GO:0004657 proline dehydrogenase activity

Biological Process

• GO:0006562 proline catabolic process

External links

• PDB: RCSB:8dkp, PDBe:8dkp, PDBj:8dkp
• PDBsum: 8dkp
• PubMed: 36448708
• UniProt: F7X6I3