Structure of PDB 7x5n Chain A Binding Site BS03

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 ID5M5
InChIInChI=1S/C24H24N4O2/c1-14(2)24(20(12-25)22(26)30-23-21(24)15(3)27-28-23)19-10-16(13-29)9-18(11-19)17-7-5-4-6-8-17/h4-11,14,29H,13,26H2,1-3H3,(H,27,28)/t24-/m0/s1
InChIKeyVVVOFJZXKJKHTD-DEOSSOPVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)[C@]1(c2cc(CO)cc(c2)c3ccccc3)C(=C(N)Oc4[nH]nc(C)c14)C#N
OpenEye OEToolkits 2.0.7Cc1c2c([nH]n1)OC(=C([C@@]2(c3cc(cc(c3)c4ccccc4)CO)C(C)C)C#N)N
OpenEye OEToolkits 2.0.7Cc1c2c([nH]n1)OC(=C(C2(c3cc(cc(c3)c4ccccc4)CO)C(C)C)C#N)N
CACTVS 3.385CC(C)[C]1(c2cc(CO)cc(c2)c3ccccc3)C(=C(N)Oc4[nH]nc(C)c14)C#N
FormulaC24 H24 N4 O2
Name(4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain7x5n Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		E53 Y60 Y61
Binding residue
(residue number reindexed from 1)		E51 Y58 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

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

[Back to BioLiP]