Structure of PDB 1eji Chain D Binding Site BS02

Receptor Information
>1eji Chain D (length=478) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MADRDATLWASHEKMLSQPLKDSDAEVYSIIKKESNRQRVGLELIASENF
ASRAVLEALGSSLNNKYSEGYPGQRYYGGTEFIDELEMLCQKRALQAYHL
DPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTD
KKKISATSIFFESMPYKVYPETGYINYDQLEENASLFHPKLIIAGTSCYS
RNLDYARLRKIADDNGAYLMADMAHISGLVAAGVVPSPFEHCHVVTTTTH
KTLRGCRAGMIFYRKGVRSVDPKTGKETYYELESLINSAVFPGLQGGPHN
HAIAGVAVALKQAMTTEFKIYQLQVLANCRALSDALTELGYKIVTGGSDN
HLILMDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTP
ALTSRGLLEEDFQKVAHFIHRGIELTLQIQSHMATKATLKEFKEKLAGDE
KIQSAVATLREEVENFASNFSLPGLPDF
Ligand information
Ligand IDPLG
InChIInChI=1S/C10H15N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2,11,15H,3-5H2,1H3,(H,13,14)(H2,16,17,18)
InChIKeyFEVQWBMNLWUBTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNCC(O)=O)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNCC(=O)O)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
FormulaC10 H15 N2 O7 P
NameN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE];
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
ChEMBL
DrugBankDB02824
ZINCZINC000002046831
PDB chain1eji Chain D Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1eji Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		S53 S119 G120 S121 H148 H151 D228 A230 H231 K257 R402
Binding residue
(residue number reindexed from 1)		S47 S113 G114 S115 H142 H145 D222 A224 H225 K251 R396
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y73 E75 D228 T254 K257 R263
Catalytic site (residue number reindexed from 1) Y67 E69 D222 T248 K251 R257
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0048027 mRNA 5'-UTR binding
GO:0070905 serine binding
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0009113 purine nucleobase biosynthetic process
GO:0017148 negative regulation of translation
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
GO:0051289 protein homotetramerization
GO:1904482 cellular response to tetrahydrofolate
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
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:1eji, PDBe:1eji, PDBj:1eji
PDBsum1eji
PubMed11063567
UniProtP50431|GLYC_MOUSE Serine hydroxymethyltransferase, cytosolic (Gene Name=Shmt1)

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