Structure of PDB 8st6 Chain A Binding Site BS01

Receptor Information

>8st6 Chain A (length=204) Species: 467705 (Streptococcus gordonii str. Challis substr. CH1)

EAPQVKSGDYVVYRGESFEYYAEITDNSGQVNRVVIRNVEGGANSTYLSP
NWVKYSTENLGRPGNATVQNPLRTRIFGEVPLNEIVNEKSYYTRYIVAWD
PSGNATQMVDNANRNGLERFVLTVKSQNEKYDPAESSVTYVNNLSNLSTS
EREAVAAAVRAANPNIPPTAKITVSQNGTVTITYPDKSTDTIPANRVVKD
LQIS

Ligand information

• Ligand ID: USR
• InChI: InChI=1S/C18H31NO15/c1-31-16-13(28)15(12(27)8(4-21)32-16)34-18(17(29)30)2-6(23)10(19-9(25)5-22)14(33-18)11(26)7(24)3-20/h6-8,10-16,20-24,26-28H,2-5H2,1H3,(H,19,25)(H,29,30)/t6-,7-,8+,10+,11+,12-,13-,14+,15-,16+,18-/m0/s1
• InChIKey: UWADXVSOESDFFH-VKYAEBFESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: COC1C(C(C(C(O1)CO)O)OC2(CC(C(C(O2)C(C(CO)O)O)NC(=O)CO)O)C(=O)O)O
  CACTVS 3.385: CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O[C@@]2(C[C@H](O)[C@H](NC(=O)CO)[C@@H](O2)[C@H](O)[C@@H](O)CO)C(O)=O)[C@@H]1O
  CACTVS 3.385: CO[CH]1O[CH](CO)[CH](O)[CH](O[C]2(C[CH](O)[CH](NC(=O)CO)[CH](O2)[CH](O)[CH](O)CO)C(O)=O)[CH]1O
  ACDLabs 12.01: OCC(O)C(O)C1OC(OC2C(O)C(OC)OC(CO)C2O)(CC(O)C1NC(=O)CO)C(=O)O
  OpenEye OEToolkits 2.0.7: CO[C@H]1[C@@H]([C@@H]([C@H]([C@H](O1)CO)O)O[C@@]2(C[C@@H]([C@H]([C@H](O2)[C@H]([C@H](CO)O)O)NC(=O)CO)O)C(=O)O)O
• Formula: C18 H31 N O15
• Name: methyl 3-O-[3,5-dideoxy-5-(2-hydroxyacetamido)-L-glycero-alpha-D-gulo-non-2-ulopyranonosyl]-beta-D-talopyranoside
• PDB chain: 8st6 Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8st6 Hsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe
• Resolution: 1.45 Å
• Binding residue (original residue number in PDB): V285 K335 Y337 Y338 T339 R340 Y341 D356
• Binding residue (residue number reindexed from 1): V39 K89 Y91 Y92 T93 R94 Y95 D110
• Annotation score: 1

External links

• PDB: RCSB:8st6, PDBe:8st6, PDBj:8st6
• PDBsum: 8st6
• UniProt: A8AWU7|HSA_STRGC Streptococcal hemagglutinin (Gene Name=hsa)