Structure of PDB 6vgf Chain C Binding Site BS01

Receptor Information
>6vgf Chain C (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 C Residue 301 [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]
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 Y125 N127 S211
Binding residue
(residue number reindexed from 1)
D80 D83 G103 Y125 N127 S211
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

[Back to BioLiP]