Structure of PDB 8i7h Chain A Binding Site BS02

Receptor Information

>8i7h Chain A (length=297) Species: 585 (Proteus vulgaris)

TKIKVAIVGYGNIGRFALEAVQAAQDFELVGVVRRDINNVPEELQNITVT
NDIKTLGDVDVALLCSPTRAIKELAKSILSLGINTVDSFDVHSEIVSLKT
ELDDVAKKHDRVAVISAGWDPGSDSIVRTLMLAMAPKGITYTNFGPGMSM
GHSVAAKAIEGVKDALSMTIPLGTGVHRRMVYVELEAGANFNQVEQAIKA
DSYFSSDETHVKQVDSVDSLKDVGHGVHMTHKGVSGKTHNQLFEYSMRIN
NPALTSQFMVSAARASMKQRAGAYTVIEIPPVDFLAGDLNTLIAKLV

Ligand information

• Ligand ID: API
• InChI: InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
• InChIKey: GMKMEZVLHJARHF-SYDPRGILSA-N
• SMILES:
  CACTVS 3.370: N[CH](CCC[CH](N)C(O)=O)C(O)=O
  OpenEye OEToolkits 1.7.2: C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
  OpenEye OEToolkits 1.7.2: C(CC(C(=O)O)N)CC(C(=O)O)N
  CACTVS 3.370: N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
  ACDLabs 12.01: O=C(O)C(N)CCCC(C(=O)O)N
• Formula: C7 H14 N2 O4
• Name: 2,6-DIAMINOPIMELIC ACID
• ChEMBL: CHEMBL415306
• ZINC: ZINC000001532722
• PDB chain: 8i7h Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i7h Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope
• Resolution: 3.02 Å
• Binding residue (original residue number in PDB): W121 D122 F146 T257
• Binding residue (residue number reindexed from 1): W119 D120 F144 T255
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 1.4.1.16: diaminopimelate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0047850 diaminopimelate dehydrogenase activity

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate
• GO:0019877 diaminopimelate biosynthetic process

External links

• PDB: RCSB:8i7h, PDBe:8i7h, PDBj:8i7h
• PDBsum: 8i7h
• UniProt: A0A379F6K8