Structure of PDB 4cmd Chain A Binding Site BS01

Receptor Information

>4cmd Chain A (length=322)

MATMDKVFAGYAERQAVLEASKNPLAKGVAWIQGELVPLHEARIPLLDQG
FMHSDLTYDVPSVWDGRFFRLEDHLNRLEASCKKMRLRMPLPREEVIKTL
VDMVAKSGIRDAFVELIVTRGLTGVRGAKPEELLNNNLYMFIQPYVWVMD
PDVQYTGGRAIVARTVRRVPPGSIDPTIKNLQWGDLVRGLFEANDRGATY
PFLTDGDANLTEGSGFNVVLIKDGVLYTPDRGVLQGITRKSVIDAARSCG
YEIRVEHVPIEATYQADEILMCTTAGGIMPITTLDDKPVKDGKVGPITKA
IWDRYWAMHWEDEFSFKINYLE

Ligand information

• Ligand ID: PLP
• InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
• InChIKey: NGVDGCNFYWLIFO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C=O)C
• Formula: C8 H10 N O6 P
• Name: PYRIDOXAL-5'-PHOSPHATE;
  VITAMIN B6 Phosphate
• ChEMBL: CHEMBL82202
• DrugBank: DB00114
• ZINC: ZINC000001532514
• PDB chain: 4cmd Chain A Residue 1179

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cmd The Substrate Specificity, Enantioselectivity and Structure of the (R)-Selective Amine:Pyruvate Transaminase from Nectria Haematococca.
• Resolution: 1.68 Å
• Binding residue (original residue number in PDB): R77 K179 E212 G215 F216 L234 G236 I237 T238 T274
• Binding residue (residue number reindexed from 1): R77 K179 E212 G215 F216 L234 G236 I237 T238 T274
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y58 V60 K179 E212 L234
• Catalytic site (residue number reindexed from 1): Y58 V60 K179 E212 L234
• Enzyme Commision number: 2.6.1.42: branched-chain-amino-acid transaminase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

Biological Process

• GO:0019752 carboxylic acid metabolic process
• GO:0046394 carboxylic acid biosynthetic process

External links

• PDB: RCSB:4cmd, PDBe:4cmd, PDBj:4cmd
• PDBsum: 4cmd
• PubMed: 24618038
• UniProt: C7YVL8