Structure of PDB 6vgf Chain A Binding Site BS01

Receptor Information
>6vgf Chain A (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 IDWA3
InChIInChI=1S/C42H68N6O27S4/c49-5-15-21(53)27(59)33(65)39(71-15)78-41-35(67)29(61)23(55)17(73-41)9-76-7-11-1-47(45-43-11)3-13-19(51)25(57)31(63)37(69-13)75-38-32(64)26(58)20(52)14(70-38)4-48-2-12(44-46-48)8-77-10-18-24(56)30(62)36(68)42(74-18)79-40-34(66)28(60)22(54)16(6-50)72-40/h1-2,13-42,49-68H,3-10H2/t13-,14-,15-,16+,17-,18-,19-,20-,21+,22+,23-,24-,25+,26+,27+,28+,29+,30+,31-,32-,33-,34-,35-,36-,37-,38-,39+,40+,41+,42+/m1/s1
InChIKeyBEFBDKWEVXNDEF-GYSUOSJOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H]1O[C@@H](S[C@@H]2O[C@H](CSCc3cn(C[C@H]4O[C@H](O[C@H]5O[C@H](Cn6cc(CSC[C@H]7O[C@@H](S[C@@H]8O[C@@H](CO)[C@H](O)[C@H](O)[C@H]8O)[C@H](O)[C@@H](O)[C@@H]7O)nn6)[C@@H](O)[C@H](O)[C@H]5O)[C@H](O)[C@@H](O)[C@@H]4O)nn3)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@H]1O
OpenEye OEToolkits 2.0.7c1c(nnn1C[C@@H]2[C@H]([C@@H]([C@H]([C@H](O2)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)Cn4cc(nn4)CSC[C@@H]5[C@H]([C@@H]([C@H]([C@@H](O5)S[C@H]6[C@@H]([C@H]([C@H]([C@H](O6)CO)O)O)O)O)O)O)O)O)O)O)O)O)CSC[C@@H]7[C@H]([C@@H]([C@H]([C@@H](O7)S[C@H]8[C@@H]([C@H]([C@H]([C@H](O8)CO)O)O)O)O)O)O
OpenEye OEToolkits 2.0.7c1c(nnn1CC2C(C(C(C(O2)OC3C(C(C(C(O3)Cn4cc(nn4)CSCC5C(C(C(C(O5)SC6C(C(C(C(O6)CO)O)O)O)O)O)O)O)O)O)O)O)O)CSCC7C(C(C(C(O7)SC8C(C(C(C(O8)CO)O)O)O)O)O)O
CACTVS 3.385OC[CH]1O[CH](S[CH]2O[CH](CSCc3cn(C[CH]4O[CH](O[CH]5O[CH](Cn6cc(CSC[CH]7O[CH](S[CH]8O[CH](CO)[CH](O)[CH](O)[CH]8O)[CH](O)[CH](O)[CH]7O)nn6)[CH](O)[CH](O)[CH]5O)[CH](O)[CH](O)[CH]4O)nn3)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01C1(C(C(O)C(O)C(O1)CO)O)SC2OC(C(C(C2O)O)O)CSCc8nnn(CC3OC(C(C(C3O)O)O)OC4OC(C(C(C4O)O)O)Cn5cc(nn5)CSCC7C(C(O)C(O)C(SC6C(C(O)C(O)C(CO)O6)O)O7)O)c8
FormulaC42 H68 N6 O27 S4
Name(2S,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({4-[({[(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-2-yl]methyl}sulfanyl)methyl]-1H-1,2,3-triazol-1-yl}methyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol
ChEMBL
DrugBank
ZINC
PDB chain6vgf Chain A 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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PDB6vgf 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.
Resolution1.83 Å
Binding residue
(original residue number in PDB)
D80 D83 G103 G104 Y125 N127 S211 G214
Binding residue
(residue number reindexed from 1)
D80 D83 G103 G104 Y125 N127 S211 G214
Annotation score1
Binding affinityMOAD: Kd=180uM
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:6vgf, PDBe:6vgf, PDBj:6vgf
PDBsum6vgf
PubMed33135679
UniProtP02872|LECG_ARAHY Galactose-binding lectin

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