Structure of PDB 6m4n Chain F Binding Site BS01

Receptor Information
>6m4n Chain F (length=491) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IHHVTQNGGLYKRPFNEAFEETPMLVAVLTYVGYGVLTLFGYLRDFLRYW
RCHHATEREEQKDFVSLYQDFENFYTRNLYMRIRDNWNRPICSVPGARVD
IMERQSHDYNWSFKYTGNIIKGVINMGSYNYLGFARNTGSCQEAAAKVLE
EYGAGVCSTRQEIGNLDKHEELEELVARFLGVEAAMAYGMGFATNSMNIP
ALVGKGCLILSDELNHASLVLGARLSGATIRIFKHNNMQSLEKLLKDAIV
YGQPRTRRPWKKILILVEGIYSMEGSIVRLPEVIALKKKYKAYLYLDEAH
SIGALGPTGRGVVEYFGLDPEDVDVMMGTFTKSFGASGGYIGGKKELIDY
LRTHSHSAVYATSLSPPVVEQIITSMKCIMGSLGKECVQQLAENTRYFRR
RLKEMGFIIYGNEDSPVVPLMLYMPAKIGAFGREMLKRNIGVVVVGFPAT
PIIESRARFCLSAAHTKEILDTALKEIDEVGDLLQLKYSRH
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain6m4n Chain F Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6m4n Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		G238 H263 S265 E315 A346 H347 T376 T378 K379
Binding residue
(residue number reindexed from 1)		G191 H216 S218 E268 A299 H300 T329 T331 K332
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.50: serine C-palmitoyltransferase.
Gene Ontology
Molecular Function
GO:0004758 serine C-palmitoyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006665 sphingolipid metabolic process
GO:0006686 sphingomyelin biosynthetic process
GO:0009058 biosynthetic process
GO:0030148 sphingolipid biosynthetic process
GO:0046511 sphinganine biosynthetic process
GO:0046512 sphingosine biosynthetic process
GO:0046513 ceramide biosynthetic process
GO:0060612 adipose tissue development
GO:1904504 positive regulation of lipophagy
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0017059 serine palmitoyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6m4n, PDBe:6m4n, PDBj:6m4n
PDBsum6m4n
PubMed33558762
UniProtO15270|SPTC2_HUMAN Serine palmitoyltransferase 2 (Gene Name=SPTLC2)

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