Structure of PDB 6vc4 Chain D Binding Site BS01

Receptor Information
>6vc4 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 IDQWG
InChIInChI=1S/C22H37N3O14S2/c1-36-20-17(33)14(30)11(27)8(37-20)3-25-2-7(23-24-25)5-40-6-10-13(29)16(32)19(35)22(39-10)41-21-18(34)15(31)12(28)9(4-26)38-21/h2,8-22,26-35H,3-6H2,1H3/t8-,9-,10-,11-,12+,13-,14+,15+,16+,17-,18-,19-,20+,21+,22+/m1/s1
InChIKeyNRANZAMORPDRSV-CBEZMCEXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COC1C(C(C(C(O1)Cn2cc(nn2)CSCC3C(C(C(C(O3)SC4C(C(C(C(O4)CO)O)O)O)O)O)O)O)O)O
OpenEye OEToolkits 2.0.7CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)Cn2cc(nn2)CSC[C@@H]3[C@H]([C@@H]([C@H]([C@@H](O3)S[C@H]4[C@@H]([C@H]([C@H]([C@H](O4)CO)O)O)O)O)O)O)O)O)O
CACTVS 3.385CO[CH]1O[CH](Cn2cc(CSC[CH]3O[CH](S[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH](O)[CH]3O)nn2)[CH](O)[CH](O)[CH]1O
CACTVS 3.385CO[C@H]1O[C@H](Cn2cc(CSC[C@H]3O[C@@H](S[C@@H]4O[C@H](CO)[C@H](O)[C@H](O)[C@H]4O)[C@H](O)[C@@H](O)[C@@H]3O)nn2)[C@@H](O)[C@H](O)[C@H]1O
ACDLabs 12.01n1nn(cc1CSCC2C(C(C(C(O2)SC3C(C(C(C(CO)O3)O)O)O)O)O)O)CC4C(O)C(O)C(C(OC)O4)O
FormulaC22 H37 N3 O14 S2
Name(2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-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 (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain6vc4 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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PDB6vc4 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.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
D80 D83 G103 G104 Y125 N127 S211
Binding residue
(residue number reindexed from 1)
D80 D83 G103 G104 Y125 N127 S211
Annotation score1
Binding affinityMOAD: Kd=360uM
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:6vc4, PDBe:6vc4, PDBj:6vc4
PDBsum6vc4
PubMed33135679
UniProtP02872|LECG_ARAHY Galactose-binding lectin

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