Structure of PDB 7v3d Chain A Binding Site BS01

Receptor Information
>7v3d 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 chain7v3d Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7v3d Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		L117 G121 H122 L123 K342 S344 P352 F353 R359
Binding residue
(residue number reindexed from 1)		L115 G119 H120 L121 K340 S342 P350 F351 R357
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:7v3d, PDBe:7v3d, PDBj:7v3d
PDBsum7v3d
PubMed35739195
UniProtI3U4H4

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