Structure of PDB 5ody Chain A Binding Site BS01

Receptor Information
>5ody Chain A (length=138) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLIVPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPR
FNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVA
VNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI
Ligand information
Ligand ID9SK
InChIInChI=1S/C30H28F5N3O11S/c31-13-1-2-17-12(20(13)34)3-11(28(45)47-17)9-46-27-24(42)19(8-40)49-30(26(27)44)50-29-25(43)22(23(41)18(7-39)48-29)38-6-16(36-37-38)10-4-14(32)21(35)15(33)5-10/h1-6,18-19,22-27,29-30,39-44H,7-9H2/t18-,19-,22+,23+,24+,25-,26-,27+,29+,30+/m1/s1
InChIKeyVZWCREWZIXJWMB-DYBDPJTGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(c2c1OC(=O)C(=C2)CO[C@H]3[C@H]([C@H](O[C@H]([C@@H]3O)S[C@H]4[C@@H]([C@H]([C@H]([C@H](O4)CO)O)n5cc(nn5)c6cc(c(c(c6)F)F)F)O)CO)O)F)F
OpenEye OEToolkits 2.0.6c1cc(c(c2c1OC(=O)C(=C2)COC3C(C(OC(C3O)SC4C(C(C(C(O4)CO)O)n5cc(nn5)c6cc(c(c(c6)F)F)F)O)CO)O)F)F
CACTVS 3.385OC[CH]1O[CH](S[CH]2O[CH](CO)[CH](O)[CH]([CH]2O)n3cc(nn3)c4cc(F)c(F)c(F)c4)[CH](O)[CH](OCC5=Cc6c(F)c(F)ccc6OC5=O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@@H](S[C@@H]2O[C@H](CO)[C@H](O)[C@@H]([C@H]2O)n3cc(nn3)c4cc(F)c(F)c(F)c4)[C@H](O)[C@@H](OCC5=Cc6c(F)c(F)ccc6OC5=O)[C@H]1O
FormulaC30 H28 F5 N3 O11 S
Name5,6-bis(fluoranyl)-3-[[(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-2-yl]sulfanyl-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]chromen-2-one
ChEMBL
DrugBank
ZINC
PDB chain5ody 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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PDB5ody Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity.
Resolution1.149 Å
Binding residue
(original residue number in PDB)
R144 I145 A146 H158 N160 R162 W181 E184 R186 S237 G238
Binding residue
(residue number reindexed from 1)
R32 I33 A34 H46 N48 R50 W69 E72 R74 S125 G126
Annotation score1
Binding affinityMOAD: Kd=4nM
PDBbind-CN: -logKd/Ki=8.40,Kd=4.0nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0030246 carbohydrate binding

View graph for
Molecular Function
External links
PDB RCSB:5ody, PDBe:5ody, PDBj:5ody
PDBsum5ody
PubMed29284090
UniProtP17931|LEG3_HUMAN Galectin-3 (Gene Name=LGALS3)

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