Structure of PDB 1oda Chain A Binding Site BS01

Receptor Information

>1oda Chain A (length=116) Species: 10090 (Mus musculus)

TWGVSSPKNVQGLSGSCLLIPCIFSYPADVPVGITAIWYYDYSGKRQVVI
HSGDPKLVDKRFRGRAELMGNMDHKVCNLLLKDLKPEDSGTYNFRFEISD
SNRWLDVKGTTVTVTT

Ligand information

• Ligand ID: BDU
• InChI: InChI=1S/C25H30N2O9/c1-14(28)27-20-18(29)12-25(35-2,24(33)34)36-22(20)21(31)19(30)13-26-23(32)17-10-8-16(9-11-17)15-6-4-3-5-7-15/h3-11,18-22,29-31H,12-13H2,1-2H3,(H,26,32)(H,27,28)(H,33,34)/t18-,19+,20+,21+,22+,25+/m0/s1
• InChIKey: WBWCOQWBSRYCDR-TUTCKEIYSA-N
• SMILES:
  ACDLabs 10.04: O=C(c2ccc(c1ccccc1)cc2)NCC(O)C(O)C3OC(OC)(C(=O)O)CC(O)C3NC(=O)C
  CACTVS 3.341: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CNC(=O)c2ccc(cc2)c3ccccc3)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CNC(=O)c2ccc(cc2)c3ccccc3)O)O)(C(=O)O)OC)O
  CACTVS 3.341: CO[C]1(C[CH](O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)CNC(=O)c2ccc(cc2)c3ccccc3)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CNC(=O)c2ccc(cc2)c3ccccc3)O)O)(C(=O)O)OC)O
• Formula: C25 H30 N2 O9
• Name: ME-A-9-N-(BIPHENYL-4-CARBONYL)-AMINO-9-DEOXY-NEU5AC
• ZINC: ZINC000058626773
• PDB chain: 1oda Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1oda Structure Guided Design of Sialic Acid-Based Siglec Inhibitors and Crystallographic Analysis in Complex with Sialoadhesin
• Resolution: 3.31 Å
• Binding residue (original residue number in PDB): W2 R97 S103 R105 W106 L107 V109 T118
• Binding residue (residue number reindexed from 1): W2 R95 S101 R103 W104 L105 V107 T116
• Annotation score: 1

External links

• PDB: RCSB:1oda, PDBe:1oda, PDBj:1oda
• PDBsum: 1oda
• PubMed: 12737821
• UniProt: Q62230|SN_MOUSE Sialoadhesin (Gene Name=Siglec1)