Structure of PDB 8d2v Chain A Binding Site BS01

Receptor Information
>8d2v Chain A (length=460) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRLSVCSKLCYAIGGAPYQITGCAIGFFLQIYLLDVALLDPFYASIILFV
GRAWDAVTDPTVGFLVSRTPWTRFGRMMPWIVLSTPFAVLCYFLIWYVPS
VDQGKVVWYLIFYCCFQTLQTCFHVPYSALTMFISTEQKERDSATAYRMT
VEVLGTLIGTAIQGQIVGMANAPCISTEIDLQHVSLQDLRNAYMIASGVI
CAIYVVCAVVLFLGVKEQKDTCRVRTEPMSFFQGICMVMGHGPYAKLVMG
FLFTSLAFMLLEGNFALFCIYNLGFRNDFQNVLLVIMLSATLAIPFWQWF
LTKFGKKTAVYIGTTSVVPFLISVVLVPSSLAVTYIASFAAGVSVAAAFL
LPWSMLPDVVDDFKVQNPESQGHEAIFYSFYVFFTKFASGVSLGVSTLSL
DFAGYVTRGCTQPGEVKLTLKILVSAAPIVLIIIGLLIFISYPINEEKRQ
GNRKLLNEQR
Ligand information
Ligand IDZGS
InChIInChI=1S/C26H48NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-26(29)32-23-25(28)24-34-35(30,31)33-22-21-27(2,3)4/h6-7,9-10,12-13,25,28H,5,8,11,14-24H2,1-4H3/p+1/b7-6-,10-9-,13-12-/t25-/m1/s1
InChIKeyWKQNRCYKYCKESD-YVHLTTHBSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01C[N+](C)(C)CCOP(O)(=O)OCC(O)COC(=O)CCCCCCC/C=C\C/C=C\C/C=C\CC
OpenEye OEToolkits 2.0.7CCC=CCC=CCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N+](C)(C)C)O
CACTVS 3.385CCC=CCC=CCC=CCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)OCC[N+](C)(C)C
OpenEye OEToolkits 2.0.7CC/C=C\C/C=C\C/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCC[N+](C)(C)C)O
CACTVS 3.385CC\C=C/C/C=C\C\C=C/CCCCCCCC(=O)OC[C@@H](O)CO[P](O)(=O)OCC[N+](C)(C)C
FormulaC26 H49 N O7 P
Name[(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate;
LysoPC(18:3(9Z,12Z,15Z))
ChEMBL
DrugBank
ZINCZINC000032822197
PDB chain8d2v Chain A Residue 601 [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]
PDB8d2v Lipid flipping in the omega-3 fatty-acid transporter.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		Q51 R180 M181 L308 E309 F312 I333 A388 V392 F396 W400 E421 Y425
Binding residue
(residue number reindexed from 1)		Q19 R148 M149 L261 E262 F265 I286 A341 V345 F349 W353 E374 Y378
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0015245 fatty acid transmembrane transporter activity
GO:0015293 symporter activity
GO:0051978 lysophospholipid:sodium symporter activity
Biological Process
GO:0006869 lipid transport
GO:0008643 carbohydrate transport
GO:0015908 fatty acid transport
GO:0045056 transcytosis
GO:0051977 lysophospholipid transport
GO:0055085 transmembrane transport
GO:0060856 establishment of blood-brain barrier
GO:0140329 lysophospholipid translocation
GO:1990379 lipid transport across blood-brain barrier
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8d2v, PDBe:8d2v, PDBj:8d2v
PDBsum8d2v
PubMed37156797
UniProtQ6DEJ6|NLS1B_DANRE Sodium-dependent lysophosphatidylcholine symporter 1-B (Gene Name=mfsd2ab)

[Back to BioLiP]