Structure of PDB 5kxd Chain C Binding Site BS03

Receptor Information
>5kxd Chain C (length=238) Species: 3922 (Wisteria floribunda) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KETTSFVFTRFSPDPQNLLLQGDTVVTSSGHLQLTQVKDGEPVYSSLGRA
LYYAPIHIWDSNTDTVANFVTSFSFVIDAPNKAKAADGLAFFLAPVDTEP
QKPGGLLGLFHDDRHNKSNHIVAVEFDTFKNSWDPEGTHIGINVNSIVSR
KTISWDLENNEVANVVISYQASTKTLTASLVYPSSSTSYILNDVVDLKQI
LPEYVRVGFTAASGLSKDHVETHDVLAWTFDSDLPDPS
Ligand information
Ligand ID6Y2
InChIInChI=1S/C22H31N3O13/c1-9(28)23-15-18(31)17(30)13(7-26)36-22(15)38-20-14(8-27)37-21(16(19(20)32)24-10(2)29)35-12-5-3-11(4-6-12)25(33)34/h3-6,13-22,26-27,30-32H,7-8H2,1-2H3,(H,23,28)(H,24,29)/t13-,14-,15-,16-,17+,18-,19-,20-,21-,22+/m1/s1
InChIKeyHWBFEVWOQMUQIE-BFKOZBEUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O[C@@H]2[C@H](O[C@H]([C@@H]([C@H]2O)NC(=O)C)Oc3ccc(cc3)[N+](=O)[O-])CO)CO)O)O
CACTVS 3.385CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH]2[CH](O)[CH](NC(C)=O)[CH](O[CH]2CO)Oc3ccc(cc3)[N+]([O-])=O
CACTVS 3.385CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O[C@H]2[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]2CO)Oc3ccc(cc3)[N+]([O-])=O
OpenEye OEToolkits 2.0.5CC(=O)NC1C(C(C(OC1OC2C(OC(C(C2O)NC(=O)C)Oc3ccc(cc3)[N+](=O)[O-])CO)CO)O)O
FormulaC22 H31 N3 O13
Name~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-acetamido-2-(hydroxymethyl)-6-(4-nitrophenoxy)-4-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
ChEMBL
DrugBank
ZINCZINC000263616273
PDB chain5kxd Chain C Residue 312 [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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PDB5kxd Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[ beta 14]GlcNAc), by Wisteria floribunda Agglutinin.
Resolution1.95 Å
Binding residue
(original residue number in PDB)
D117 G135 F159 N161 G244 L245 S246 H249
Binding residue
(residue number reindexed from 1)
D87 G105 F129 N131 G214 L215 S216 H219
Annotation score1
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:5kxd, PDBe:5kxd, PDBj:5kxd
PDBsum5kxd
PubMed27601469
UniProtA0A1D5B396

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