Structure of PDB 4yw1 Chain B Binding Site BS01

Receptor Information

>4yw1 Chain B (length=659) Species: 170187 (Streptococcus pneumoniae TIGR4)

ETPVLEKNNVTLTGGGENVTKELKDKFTSGDFTVVIKYNQSSEKGLQALF
GISNSKPGQQNSYVDVFLRDNGELGMEARDTSSNKNNLVSRPASVWGKYK
QEAVTNTVAVVADSVKKTYSLYANGTKVVEKKVDNFLNIKDIKGIDYYML
GGVKRAGKTAFGFNGTLENIKFFNSALDEETVKKMTTNAVTGHLIYTAND
TTGSNYFRIPVLYTFSNGRVFSSIDARYGGTHDFLNKINIATSYSDDNGK
TWTKPKLTLAFDDFAPVPLEWPREVGGRDLQISGGATYIDSVIVEKKNKQ
VLMFADVMPAGVSFREATRKDSGYKQIDGNYYLKLRKQGDTDYNYTIREN
GTVYDDRTNRPTEFSVDKNFGIKQNGNYLTVEQYSVSFENNKKTEYRNGT
KVHMNIFYKDALFKVVPTNYIAYISSNDHGESWSAPTLLPPIMGLNRNAP
YLGPGRGIIESSTGRILIPSYTGKESAFIYSDDNGASWKVKVVPLPSSWS
AEAQFVELSPGVIQAYMRTNNGKIAYLTSKDAGTTWSAPEYLKFVSNPSY
GTQLSIINYSQLIDGKKAVILSTPNSTNGRKHGQIWIGLINDDNTIDWRY
HHDVDYSNYGYSYSTLTELPNHEIGLMFEKFDSWSRNELHMKNVVPYITF
KIEDLKKNL

Ligand information

• Ligand ID: DAN
• InChI: InChI=1S/C11H17NO8/c1-4(14)12-8-5(15)2-7(11(18)19)20-10(8)9(17)6(16)3-13/h2,5-6,8-10,13,15-17H,3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,8+,9+,10+/m0/s1
• InChIKey: JINJZWSZQKHCIP-UFGQHTETSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C=1OC(C(O)C(O)CO)C(NC(=O)C)C(O)C=1
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C=C(OC1C(C(CO)O)O)C(=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
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C=C(O[CH]1[CH](O)[CH](O)CO)C(O)=O
• Formula: C11 H17 N O8
• Name: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID;
  Neu5Ac2en
• ChEMBL: CHEMBL96712
• DrugBank: DB03991
• ZINC: ZINC000004096465
• PDB chain: 4yw1 Chain B Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yw1 Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): R290 D315 I371 D372 F396 Y553 S582 R600 R662 Y695
• Binding residue (residue number reindexed from 1): R208 D233 I289 D290 F314 Y471 S500 R518 R580 Y613
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D315 E584 Y695
• Catalytic site (residue number reindexed from 1): D233 E502 Y613
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006689 ganglioside catabolic process
• GO:0009313 oligosaccharide catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0016020 membrane
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:4yw1, PDBe:4yw1, PDBj:4yw1
• PDBsum: 4yw1
• PubMed: 26370075
• UniProt: A0A0H2UQE4