Structure of PDB 6wm2 Chain R Binding Site BS01

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 IDSIA
InChIInChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
InChIKeySQVRNKJHWKZAKO-YRMXFSIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
FormulaC11 H19 N O9
NameN-acetyl-alpha-neuraminic acid;
N-acetylneuraminic acid;
sialic acid;
alpha-sialic acid;
O-SIALIC ACID
ChEMBLCHEMBL1234621
DrugBankDB03721
ZINCZINC000004081651
PDB chain6wm2 Chain W Residue 5 [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)		F618 S619
Binding residue
(residue number reindexed from 1)		F583 S584
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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