Structure of PDB 2vw1 Chain A Binding Site BS01

Receptor Information

>2vw1 Chain A (length=658) Species: 1313 (Streptococcus pneumoniae)

ISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALF
GLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHK
GQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATL
GAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDS
TQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKT
WSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGK
TILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVREN
GVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGK
QVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGT
YLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNA
TAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTS
YGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDW
KYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYI
DLEINDLT

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: 2vw1 Chain A Residue 1000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vw1 Crystal Structure of the Nanb Sialidase from Streptococcus Pneumoniae
• Resolution: 2.39 Å
• Binding residue (original residue number in PDB): R245 D270 I326 D327 N352 T539 R557 R619 Y653 W674
• Binding residue (residue number reindexed from 1): R207 D232 I288 D289 N314 T501 R519 R581 Y615 W636
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.3mM
  PDBbind-CN: -logKd/Ki=3.52,Ki=0.3mM

Enzymatic activity

• Catalytic site (original residue number in PDB): D270 E541 Y653
• Catalytic site (residue number reindexed from 1): D232 E503 Y615
• Enzyme Commision number: 3.2.1.18: exo-alpha-sialidase.

Gene Ontology

Molecular Function

• GO:0004308 exo-alpha-sialidase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:2vw1, PDBe:2vw1, PDBj:2vw1
• PDBsum: 2vw1
• PubMed: 18835278
• UniProt: Q54727|NANB_STRPN Sialidase B (Gene Name=nanB)