Structure of PDB 7k0l Chain A Binding Site BS02

Receptor Information
>7k0l Chain A (length=423) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKEC
INFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLED
RLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQ
ASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRRFIVVEGLYMN
TGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDI
DLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAI
EALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVGESLSPAFHLQLEE
STGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTV
EQTEEELERAASTIKEVAQAVLL
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7k0l Structural insights into the regulation of human serine palmitoyltransferase complexes.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		P135 F138 F337
Binding residue
(residue number reindexed from 1)		P85 F88 F287
Annotation score1
Binding affinityBindingDB: EC50=50nM
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: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:1904504 positive regulation of lipophagy
GO:1904649 regulation of fat cell apoptotic process
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0017059 serine palmitoyltransferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7k0l, PDBe:7k0l, PDBj:7k0l
PDBsum7k0l
PubMed33558761
UniProtO15269|SPTC1_HUMAN Serine palmitoyltransferase 1 (Gene Name=SPTLC1)

[Back to BioLiP]