Structure of PDB 7k0l Chain B Binding Site BS02

Receptor Information
>7k0l Chain B (length=492) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLYKRPFNEAFEETPMLVAVLTYVGYGVLTLFGYLRDFLRYWRIEKCHHA
TEREEQKDFVSLYQDFENFYTRNLYMRIRDNWNRPICSVPGARVDIMERQ
SHDYNWSFKYTGNIIKGVINMGSYNYLGFARNTGSCQEAAAKVLEEYGAG
VCSTRQEIGNLDKHEELEELVARFLGVEAAMAYGMGFATNSMNIPALVGK
GCLILSDELNHASLVLGARLSGATIRIFKHNNMQSLEKLLKDAIVYGQPR
TRRPWKKILILVEGIYSMEGSIVRLPEVIALKKKYKAYLYLDEAHSIGAL
GPTGRGVVEYFGLDPEDVDVMMGTFTKSFGASGGYIGGKKELIDYLRTHS
HSAVYATSLSPPVVEQIITSMKCIMGQDGTSLGKECVQQLAENTRYFRRR
LKEMGFIIYGNEDSPVVPLMLYMPAKIGAFGREMLKRNIGVVVVGFPATP
IIESRARFCLSAAHTKEILDTALKEIDEVGDLLQLKYSRHRL
Ligand information
Ligand IDVRP
InChIInChI=1S/C21H39NO6/c1-2-3-4-10-13-17(24)14-11-8-6-5-7-9-12-15-18(25)19(26)21(22,16-23)20(27)28/h9,12,18-19,23,25-26H,2-8,10-11,13-16,22H2,1H3,(H,27,28)/b12-9+/t18-,19+,21+/m1/s1
InChIKeyZZIKIHCNFWXKDY-GNTQXERDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(CCCC\C=C\CC(C(O)C(CO)(N)C(O)=O)O)CC(CCCCCC)=O
OpenEye OEToolkits 2.0.7CCCCCCC(=O)CCCCCC/C=C/C[C@H]([C@@H]([C@@](CO)(C(=O)O)N)O)O
OpenEye OEToolkits 2.0.7CCCCCCC(=O)CCCCCCC=CCC(C(C(CO)(C(=O)O)N)O)O
CACTVS 3.385CCCCCCC(=O)CCCCCCC=CC[CH](O)[CH](O)[C](N)(CO)C(O)=O
CACTVS 3.385CCCCCCC(=O)CCCCCC\C=C\C[C@@H](O)[C@H](O)[C@@](N)(CO)C(O)=O
FormulaC21 H39 N O6
NameMyriocin;
(2S,3R,4R,6E)-2-amino-3,4-dihydroxy-2-(hydroxymethyl)-14-oxoicos-6-enoic acid
ChEMBLCHEMBL55076
DrugBank
ZINCZINC000005782527
PDB chain7k0l Chain B Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7k0l Structural insights into the regulation of human serine palmitoyltransferase complexes.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		Y122 W134 Y176 H263 S319 H347 K379 G497 P499
Binding residue
(residue number reindexed from 1)		Y70 W82 Y124 H211 S267 H295 K327 G445 P447
Annotation score1
Binding affinityBindingDB: IC50=0.130000nM
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:7k0l, PDBe:7k0l, PDBj:7k0l
PDBsum7k0l
PubMed33558761
UniProtO15270|SPTC2_HUMAN Serine palmitoyltransferase 2 (Gene Name=SPTLC2)

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