Structure of PDB 7x5n Chain B Binding Site BS04

Receptor Information
>7x5n Chain B (length=411) Species: 1352 (Enterococcus faecium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDYKTFDPDLWAAIAKEEERQEHNLELIASENFVSEAVMAAQGSILTNKY
AEGYPGHRYYGGCEFVDIVENLAIDRAKELFGAKFANVQPHSGSQANTAA
YLALVEPGDTILGMDLSAGGHLTHGSPVNFSGKTYHFVAYGVDPTTEVID
YNVVRILARKHQPKLIVAGASAYGRTIDFAKFREIADEVGAKLMVDMAHI
AGLVAAGLHPNPVPYADITTTTTHKTLRGPRGGMILTNDEALAKKINSAV
FPGIQGGPLEHVIAGKAVAFKEALDPAFKEYSEQIIANAKAMVKVFNQAI
GTRVISGATDNHLMLIDVRELGINGKEAESILDSVNITVNKNSIPFETLS
PFKTSGIRIGTPAITTRGFKEEDAVKVAELVVKALQAKDDNAQLDEVKTG
VRELTEKFPLH
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)		S31 S93 G94 S95 H122 S172 D197 A199 H200 K226 R359
Binding residue
(residue number reindexed from 1)		S30 S92 G93 S94 H121 S171 D196 A198 H199 K225 R358
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

View graph for
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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