Structure of PDB 7yj2 Chain B Binding Site BS01

Receptor Information
>7yj2 Chain B (length=502) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IHHVTQNGGLYKRPFNEAFEETPMLVAVLTYVGYGVLTLFGYLRDFLRYW
RIEKCHHATEREEQKDFVSLYQDFENFYTRNLYMRIRDNWNRPICSVPGA
RVDIMERQSHDYNWSFKYTGNIIKGVINMGSYNYLGFARNTGSCQEAAAK
VLEEYGAGVCSTRQEIGNLDKHEELEELVARFLGVEAAMAYGMGFATNSM
NIPALVGKGCLILSDELNHASLVLGARLSGATIRIFKHNNMQSLEKLLKD
AIVYGQPRTRRPWKKILILVEGIYSMEGSIVRLPEVIALKKKYKAYLYLD
EAHSIGALGPTGRGVVEYFGLDPEDVDVMMGTFTKSFGASGGYIGGKKEL
IDYLRTHSHSAVYATSLSPPVVEQIITSMKCIMGQDGTSLGKECVQQLAE
NTRYFRRRLKEMGFIIYGNEDSPVVPLMLYMPAKIGAFGREMLKRNIGVV
VVGFPATPIIESRARFCLSAAHTKEILDTALKEIDEVGDLLQLKYSRHRL
VP
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 chain7yj2 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7yj2 Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		G238 H263 D344 T378 K379
Binding residue
(residue number reindexed from 1)		G194 H219 D300 T334 K335
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7yj2, PDBe:7yj2, PDBj:7yj2
PDBsum7yj2
PubMed37308477
UniProtO15270|SPTC2_HUMAN Serine palmitoyltransferase 2 (Gene Name=SPTLC2)

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