Structure of PDB 5kds Chain A Binding Site BS02

Receptor Information

>5kds Chain A (length=511) Species: 195103 (Clostridium perfringens ATCC 13124)

HMASVLELEMRGDSISEAKKRKVWNFQDWQITGLSARAGDKITVYVDVAE
GDPTPTLLYKQSLTQHGGATSFQLKPGKNEITIPEINYESNGIPKDVIQG
GDLFFTNYKSDSQKRAPKVRIEGASKYPVFILGKSDENEVMKELEAYVEK
IKAEPKTTPNIFAVSSNKSLEFVQATYALDWYKKNNKTPKYTAEQWDQYI
ADAMGFWGFDNSKDVNSDFNFRIMPMVKNLSGGAFMNAGNGVIGIRPGNQ
DAILAANKGWGVAHELGHNFDTGGRTIVEVTNNMMPLFFESKYKTKTRIT
DQNIWENNTYPKVGLDDYSNNELYNKADSTHLAQLAPLWQLYLYDNTFYG
KFERQFRERDFGNKNREDIYKSWVVAASDAMELDLTEFFARHGIRVDDKV
KEDLAKYPKPDKKIYYLNDLAMNYKGDGFTENAKVSVSTSGSNGNIKLSF
SVDDENKDNILGYEIRRDGKYVGFTSNDSFVDTKSNLDEDGVYVVTPYDR
KLNTLNPIEVN

Ligand information

• Ligand ID: SIA
• InChI: InChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
• InChIKey: SQVRNKJHWKZAKO-YRMXFSIDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)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](CO)O)O)(C(=O)O)O)O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H19 N O9
• Name: N-acetyl-alpha-neuraminic acid;
  N-acetylneuraminic acid;
  sialic acid;
  alpha-sialic acid;
  O-SIALIC ACID
• ChEMBL: CHEMBL1234621
• DrugBank: DB03721
• ZINC: ZINC000004081651
• PDB chain: 5kds Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kds Recognition of protein-linked glycans as a determinant of peptidase activity.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): F727 N749 G751 G753 V754
• Binding residue (residue number reindexed from 1): F235 N257 G259 G261 V262
• Annotation score: 4

External links

• PDB: RCSB:5kds, PDBe:5kds, PDBj:5kds
• PDBsum: 5kds
• PubMed: 28096352
• UniProt: A0A0H2YN38