Structure of PDB 6wm2 Chain R Binding Site BS04

Receptor Information
>6wm2 Chain R (length=753) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELFRSEEMTLAQLFLQSEAAYCCVSELGELGKVQFRDLNPDVNVFQRKFV
NEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFE
KIENELKEINTNQEALKRNFLELTELKFILRKTGFVAGVINRERIPTFER
MLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKK
ICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQA
AAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQF
ALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTYGFQNIVDAYGIGT
YREINPAPYTIITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKN
ENEMFSTVFSGRYIILLMGVFSMYTGLIYNDCFSKSLNIFGSSWSVRPMF
TYNWTEETLRGNPVLQLNPALPGVFGGPYPFGIDPIWNIATNKLTFLNSF
KMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMTSLFGY
LVILIFYKWTAYDAHTSENAPSLLIHFINMFLFSYPESGYSMLYSGQKGI
QCFLVVVALLCVPWMLLFKPLVLRRQYLRRKFDFGDTMVHQAIHTIEYCL
GCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLSVKSLAGGLVLFFFF
TAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYSGTGFKFLPFSFEH
IRE
Ligand information
Ligand IDCLR
InChIInChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyHVYWMOMLDIMFJA-DPAQBDIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
CACTVS 3.341CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
OpenEye OEToolkits 1.5.0CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
CACTVS 3.341CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
FormulaC27 H46 O
NameCHOLESTEROL
ChEMBLCHEMBL112570
DrugBankDB04540
ZINCZINC000003875383
PDB chain6wm2 Chain R Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6wm2 Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		F370 L452 F456
Binding residue
(residue number reindexed from 1)		F335 L417 F421
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0046961 proton-transporting ATPase activity, rotational mechanism
GO:0051117 ATPase binding
Biological Process
GO:0007035 vacuolar acidification
GO:0007042 lysosomal lumen acidification
GO:0016241 regulation of macroautophagy
GO:0048388 endosomal lumen acidification
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
GO:0005737 cytoplasm
GO:0005765 lysosomal membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016471 vacuolar proton-transporting V-type ATPase complex
GO:0016607 nuclear speck
GO:0030665 clathrin-coated vesicle membrane
GO:0030667 secretory granule membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0033176 proton-transporting V-type ATPase complex
GO:0033179 proton-transporting V-type ATPase, V0 domain
GO:0042470 melanosome
GO:0043231 intracellular membrane-bounded organelle
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0101003 ficolin-1-rich granule membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wm2, PDBe:6wm2, PDBj:6wm2
PDBsum6wm2
PubMed33065002
UniProtQ93050|VPP1_HUMAN V-type proton ATPase 116 kDa subunit a 1 (Gene Name=ATP6V0A1)

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