Structure of PDB 4h3d Chain A Binding Site BS01

Receptor Information

>4h3d Chain A (length=252) Species: 272563 (Clostridioides difficile 630)

MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRV
DFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTT
LNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTP
KKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRP
IITMSMSGMGVISRLCGEIFGSALTFGAAKAPGQISFKELNSVLNLLHKS
IN

Ligand information

• Ligand ID: SHL
• InChI: InChI=1S/C7H6O5/c1-3-6(9)4(8)2-5(12-3)7(10)11/h2,9H,1H3,(H,10,11)
• InChIKey: ANRPPKUCFMTTIH-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C1C=C(OC(=C1O)C)C(=O)O
  OpenEye OEToolkits 1.7.6: CC1=C(C(=O)C=C(O1)C(=O)O)O
  CACTVS 3.370: CC1=C(O)C(=O)C=C(O1)C(O)=O
• Formula: C7 H6 O5
• Name: 5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid;
  Comenic acid
• PDB chain: 4h3d Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4h3d 1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): H144 K171 M204 R214 F226 Q237
• Binding residue (residue number reindexed from 1): H144 K171 M204 R214 F226 Q234
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E87 H144 K171
• Catalytic site (residue number reindexed from 1): E87 H144 K171
• Enzyme Commision number: 4.2.1.10: 3-dehydroquinate dehydratase.

Gene Ontology

Molecular Function

• GO:0003855 3-dehydroquinate dehydratase activity
• GO:0016829 lyase activity

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0009073 aromatic amino acid family biosynthetic process
• GO:0009423 chorismate biosynthetic process
• GO:0046279 3,4-dihydroxybenzoate biosynthetic process

External links

• PDB: RCSB:4h3d, PDBe:4h3d, PDBj:4h3d
• PDBsum: 4h3d
• UniProt: Q186A6|AROD_CLOD6 3-dehydroquinate dehydratase (Gene Name=aroD)