Structure of PDB 6wm2 Chain 3 Binding Site BS01

Receptor Information
>6wm2 Chain 3 (length=150) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEQIMKS
IIPVVMAGIIAIYGLVVAVLIANSLNDDISLYKSFLQLGAGLSVGLSGLA
AGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK
Ligand information
Ligand IDWSS
InChIInChI=1S/C44H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-43(46)50-40-42(41-52-54(48,49)51-39-38-45(3,4)5)53-44(47)37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h20-23,42H,6-19,24-41H2,1-5H3/p+1/b22-20+,23-21-/t42-/m1/s1
InChIKeySNKAWJBJQDLSFF-TWROKUQOSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N+](C)(C)C)OC(=O)CCCCCCCC=CCCCCCCCC
ACDLabs 12.01C(OP(=O)(O)OCC[N+](C)(C)C)C(COC(=O)CCCCCCC[C@H]=CCCCCCCCC)OC(CCCCCCC[C@H]=CCCCCCCCC)=O
OpenEye OEToolkits 2.0.7CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCC[N+](C)(C)C)OC(=O)CCCCCCC/C=C\CCCCCCCC
CACTVS 3.385CCCCCCCCC=CCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OCC[N+](C)(C)C)OC(=O)CCCCCCCC=CCCCCCCCC
CACTVS 3.385CCCCCCCC\C=C\CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OCC[N+](C)(C)C)OC(=O)CCCCCCC\C=C/CCCCCCCC
FormulaC44 H85 N O8 P
Nametri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium
ChEMBL
DrugBank
ZINCZINC000085546476
PDB chain6wm2 Chain 3 Residue 201 [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]
PDB6wm2 Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		E9 Y10
Binding residue
(residue number reindexed from 1)		E4 Y5
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0015078 proton transmembrane transporter activity
GO:0031625 ubiquitin protein ligase binding
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0007035 vacuolar acidification
GO:0007042 lysosomal lumen acidification
GO:0015986 proton motive force-driven ATP synthesis
GO:0016241 regulation of macroautophagy
GO:0030177 positive regulation of Wnt signaling pathway
GO:0048388 endosomal lumen acidification
GO:0051452 intracellular pH reduction
GO:0061795 Golgi lumen acidification
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000139 Golgi membrane
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
GO:0005765 lysosomal membrane
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030665 clathrin-coated vesicle membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0033176 proton-transporting V-type ATPase complex
GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain
GO:0033179 proton-transporting V-type ATPase, V0 domain
GO:0035577 azurophil granule membrane
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wm2, PDBe:6wm2, PDBj:6wm2
PDBsum6wm2
PubMed33065002
UniProtP27449|VATL_HUMAN V-type proton ATPase 16 kDa proteolipid subunit c (Gene Name=ATP6V0C)

[Back to BioLiP]