Structure of PDB 5kxd Chain A Binding Site BS03

Receptor Information

>5kxd Chain A (length=238) Species: 3922 (Wisteria floribunda)

KETTSFVFTRFSPDPQNLLLQGDTVVTSSGHLQLTQVKDGEPVYSSLGRA
LYYAPIHIWDSNTDTVANFVTSFSFVIDAPNKAKAADGLAFFLAPVDTEP
QKPGGLLGLFHDDRHNKSNHIVAVEFDTFKNSWDPEGTHIGINVNSIVSR
KTISWDLENNEVANVVISYQASTKTLTASLVYPSSSTSYILNDVVDLKQI
LPEYVRVGFTAASGLSKDHVETHDVLAWTFDSDLPDPS

Ligand information

• Ligand ID: 6Y2
• InChI: InChI=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
• InChIKey: HWBFEVWOQMUQIE-BFKOZBEUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.5: CC(=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 3.385: CC(=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 3.385: CC(=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 2.0.5: CC(=O)NC1C(C(C(OC1OC2C(OC(C(C2O)NC(=O)C)Oc3ccc(cc3)[N+](=O)[O-])CO)CO)O)O
• Formula: C22 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
• ZINC: ZINC000263616273
• PDB chain: 5kxd Chain A Residue 306

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kxd Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[ beta 14]GlcNAc), by Wisteria floribunda Agglutinin.
• Resolution: 1.95 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 score: 1

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5kxd, PDBe:5kxd, PDBj:5kxd
• PDBsum: 5kxd
• PubMed: 27601469
• UniProt: A0A1D5B396