Structure of PDB 7x5n Chain A Binding Site BS04

Receptor Information
>7x5n Chain A (length=409) Species: 1352 (Enterococcus faecium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYKTFDPDLWAAIAKEEERQEHNLELIASENFVSEAVMAAQGSILTNKYA
EGYPGHRYYGGCEFVDIVENLAIDRAKELFGAKFANVQPHSGSQANTAAY
LALVEPGDTILGMDLSAGGHLTHGSPVNFSGKTYHFVAYGVDPTTEVIDY
NVVRILARKHQPKLIVAGASAYGRTIDFAKFREIADEVGAKLMVDMAHIA
GLVAAGLHPNPVPYADITTTTTHKTLRGPRGGMILTNDEALAKKINSAVF
PGIQGGPLEHVIAGKAVAFKEALDPAFKEYSEQIIANAKAMVKVFNQAIG
TRVISGATDNHLMLIDVRELGINGKEAESILDSVNITVNKNSIPFETLSP
FKTSGIRIGTPAITTRGFKEEDAVKVAELVVKALQAKDDNAQLDEVKTGV
RELTEKFPL
Ligand information
Ligand IDPLS
InChIInChI=1S/C11H17N2O8P/c1-6-10(15)8(3-13-9(4-14)11(16)17)7(2-12-6)5-21-22(18,19)20/h2,9,13-15H,3-5H2,1H3,(H,16,17)(H2,18,19,20)/t9-/m0/s1
InChIKeyODVKKQWXKRZJLG-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CO)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CO
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CO)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CO)C(O)=O)c1O
FormulaC11 H17 N2 O8 P
Name[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE;
PYRIDOXYL-SERINE-5-MONOPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000002047254
PDB chain7x5n Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7x5n Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y51 E53 Y61
Binding residue
(residue number reindexed from 1)		Y49 E51 Y59
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0030170 pyridoxal phosphate binding
GO:0050897 cobalt ion binding
GO:0070905 serine binding
Biological Process
GO:0006545 glycine biosynthetic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0008652 amino acid biosynthetic process
GO:0019264 glycine biosynthetic process from serine
GO:0032259 methylation
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7x5n, PDBe:7x5n, PDBj:7x5n
PDBsum7x5n
PubMed35739195
UniProtI3U4H4

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