Structure of PDB 2vk7 Chain A Binding Site BS02

Receptor Information

>2vk7 Chain A (length=448) Species: 1502 (Clostridium perfringens)

VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADA
PNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFL
LVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKD
SNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKT
WSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGK
QSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQV
VEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSV
INYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDW
KYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLES

Ligand information

• Ligand ID: FSI
• InChI: InChI=1S/C11H18FNO9/c1-3(15)13-5-7(18)9(12)11(21,10(19)20)22-8(5)6(17)4(16)2-14/h4-9,14,16-18,21H,2H2,1H3,(H,13,15)(H,19,20)/t4-,5-,6-,7-,8-,9-,11+/m1/s1
• InChIKey: ALJLGESFXXDPKH-RISWTRDCSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC(=O)N[C@@H]1[C@H]([C@H]([C@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)F)O
  OpenEye OEToolkits 1.7.6: CC(=O)NC1C(C(C(OC1C(C(CO)O)O)(C(=O)O)O)F)O
  CACTVS 3.370: CC(=O)N[CH]1[CH](O)[CH](F)[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  ACDLabs 12.01: O=C(O)C1(O)OC(C(NC(=O)C)C(O)C1F)C(O)C(O)CO
  CACTVS 3.370: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H18 F N O9
• Name: 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid;
  5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid;
  3-FLUOROSIALIC ACID;
  5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid;
  5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid;
  5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid
• DrugBank: DB04211
• PDB chain: 2vk7 Chain A Residue 2693

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vk7 The Structure of Clostridium Perfringens Nani Sialidase and its Catalytic Intermediates.
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): R1266 I1267 D1291 I1327 D1328 F1353 Y1485 Q1493 R1555 R1615 Y1655
• Binding residue (residue number reindexed from 1): R24 I25 D49 I85 D86 F111 Y243 Q251 R313 R373 Y413
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): A1290 D1291 E1539 Y1655
• Catalytic site (residue number reindexed from 1): A48 D49 E297 Y413
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity

External links

• PDB: RCSB:2vk7, PDBe:2vk7, PDBj:2vk7
• PDBsum: 2vk7
• PubMed: 18218621
• UniProt: Q59310