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Structure of PDB 6vav Chain D Binding Site BS01

Receptor Information
>6vav Chain D (length=232) Species: 3818 (Arachis hypogaea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAM
PVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGS
IGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKT
VPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPE
RVKFGFSASGSLGGRQIHLIRSWSFTSTLITT
Ligand information
Ligand IDQTY
InChIInChI=1S/C32H48N10O16/c43-9-17-23(49)25(51)27(53)31(57-17)35-21(47)3-1-19(45)33-5-13-7-41(39-37-13)15-11-55-30-16(12-56-29(15)30)42-8-14(38-40-42)6-34-20(46)2-4-22(48)36-32-28(54)26(52)24(50)18(10-44)58-32/h7-8,15-18,23-32,43-44,49-54H,1-6,9-12H2,(H,33,45)(H,34,46)(H,35,47)(H,36,48)/t15-,16-,17+,18+,23-,24-,25-,26-,27+,28+,29+,30+,31+,32+/m0/s1
InChIKeyWUNJKQMXDITVGU-ADJUJXGJSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1(C(C(O)C(O)C(O1)CO)O)NC(=O)CCC(NCc2nnn(c2)C3COC6C3OCC6n4nnc(c4)CNC(=O)CCC(NC5OC(CO)C(C(C5O)O)O)=O)=O
OpenEye OEToolkits 1.7.6c1c(nnn1C2COC3C2OCC3n4cc(nn4)CNC(=O)CCC(=O)NC5C(C(C(C(O5)CO)O)O)O)CNC(=O)CCC(=O)NC6C(C(C(C(O6)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH](NC(=O)CCC(=O)NCc2cn(nn2)[CH]3CO[CH]4[CH](CO[CH]34)n5cc(CNC(=O)CCC(=O)N[CH]6O[CH](CO)[CH](O)[CH](O)[CH]6O)nn5)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@@H](NC(=O)CCC(=O)NCc2cn(nn2)[C@H]3CO[C@@H]4[C@H](CO[C@H]34)n5cc(CNC(=O)CCC(=O)N[C@@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6O)nn5)[C@H](O)[C@@H](O)[C@H]1O
OpenEye OEToolkits 1.7.6c1c(nnn1[C@H]2CO[C@H]3[C@@H]2OC[C@@H]3n4cc(nn4)CNC(=O)CCC(=O)N[C@H]5[C@@H]([C@H]([C@H]([C@H](O5)CO)O)O)O)CNC(=O)CCC(=O)N[C@H]6[C@@H]([C@H]([C@H]([C@H](O6)CO)O)O)O
FormulaC32 H48 N10 O16
NameN-[[1-[(3S,3aR,6S,6aR)-6-[4-[[[4-[[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-4-oxidanylidene-butanoyl]amino]methyl]-1,2,3-triazol-1-yl]-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-3-yl]-1,2,3-triazol-4-yl]methyl]-N'-[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]butanediamide
ChEMBL
DrugBank
ZINC
PDB chain6vav Chain D Residue 301 [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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PDB6vav Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands.
Resolution1.85 Å
Binding residue
(original residue number in PDB)
D80 D83 G103 Y125 N127 S211 G213 G214
Binding residue
(residue number reindexed from 1)
D80 D83 G103 Y125 N127 S211 G213 G214
Annotation score1
Binding affinityMOAD: Kd=690uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6vav, PDBe:6vav, PDBj:6vav
PDBsum6vav
PubMed33135679
UniProtP02872|LECG_ARAHY Galactose-binding lectin

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