Structure of PDB 1vcu Chain A Binding Site BS01

Receptor Information
>1vcu Chain A (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MASLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAE
LIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFL
FFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPA
YREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSH
DHGRTWARGHFVAQDTLECQVAEVEQRVVTLNARSHLRARVQAQSTNDGL
DFQESQLVKKLVEPPPQGCQGSVISFPSPRSPAQWLLYTHPTHSWQRADL
GAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEAN
DYEEIVFLMFTLKQAFPAEY
Ligand information
Ligand IDDAN
InChIInChI=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
InChIKeyJINJZWSZQKHCIP-UFGQHTETSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C=1OC(C(O)C(O)CO)C(NC(=O)C)C(O)C=1
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C=C(OC1C(C(CO)O)O)C(=O)O)O
OpenEye OEToolkits 1.5.0CC(=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 3.341CC(=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 3.341CC(=O)N[CH]1[CH](O)C=C(O[CH]1[CH](O)[CH](O)CO)C(O)=O
FormulaC11 H17 N O8
Name2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID;
Neu5Ac2en
ChEMBLCHEMBL96712
DrugBankDB03991
ZINCZINC000004096465
PDB chain1vcu Chain A Residue 381 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vcu Crystal Structure of the Human Cytosolic Sialidase Neu2: EVIDENCE FOR THE DYNAMIC NATURE OF SUBSTRATE RECOGNITION
Resolution2.85 Å
Binding residue
(original residue number in PDB)
R21 D46 M85 E111 Y179 Y181 L217 R237 R304 Y334
Binding residue
(residue number reindexed from 1)
R21 D46 M85 E111 Y179 Y181 L217 R234 R297 Y327
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.85,Ki=0.14mM
BindingDB: Ki=25000nM,IC50=37000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D46 E218
Catalytic site (residue number reindexed from 1) D46 E218
Enzyme Commision number 3.2.1.18: exo-alpha-sialidase.
Gene Ontology
Molecular Function
GO:0004308 exo-alpha-sialidase activity
GO:0005515 protein binding
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0006516 glycoprotein catabolic process
GO:0006689 ganglioside catabolic process
GO:0009313 oligosaccharide catabolic process
GO:0016042 lipid catabolic process
GO:0046479 glycosphingolipid catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005829 cytosol
GO:0016020 membrane
GO:1902494 catalytic complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:1vcu, PDBe:1vcu, PDBj:1vcu
PDBsum1vcu
PubMed15501818
UniProtQ9Y3R4|NEUR2_HUMAN Sialidase-2 (Gene Name=NEU2)

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