Structure of PDB 4bmk Chain B Binding Site BS03

Receptor Information
>4bmk Chain B (length=386) Species: 13689 (Sphingomonas paucimobilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLG
TYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRD
FYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNA
EIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVA
KKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSASVGTVG
GFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRER
LWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGG
LYVNMALLRCSICAEHTPAQIQTVLGMFQAAGRAVG
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 chain4bmk Chain B Residue 1421 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4bmk The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin.
Resolution1.62 Å
Binding residue
(original residue number in PDB)		G134 Y135 H159 E202 D231 H234 T262 S264
Binding residue
(residue number reindexed from 1)		G113 Y114 H138 E181 D210 H213 T241 S243
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y73 H159 E202 S206 D231 H234 A265
Catalytic site (residue number reindexed from 1) Y52 H138 E181 S185 D210 H213 A244
Enzyme Commision number 2.3.1.50: serine C-palmitoyltransferase.
Gene Ontology
Molecular Function
GO:0016746 acyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006629 lipid metabolic process
GO:0006665 sphingolipid metabolic process
GO:0009058 biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4bmk, PDBe:4bmk, PDBj:4bmk
PDBsum4bmk
PubMed23957439
UniProtQ93UV0|SPT_SPHPI Serine palmitoyltransferase (Gene Name=spt)

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