Structure of PDB 4dgr Chain A Binding Site BS04

Receptor Information
>4dgr Chain A (length=389) Species: 384509 (Influenza A virus (A/tern/Australia/G70C/1975(H11N9))) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECR
FYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWS
STSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESE
CVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECS
CYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPN
DPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVP
NALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRG
RPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL
Ligand information
Ligand ID3LV
InChIInChI=1S/C20H30N2O5/c1-3-9-21(10-4-2)12-16-11-15(19(26)27)5-6-17(16)22-18(25)7-8-20(22,13-23)14-24/h5-6,11,23-24H,3-4,7-10,12-14H2,1-2H3,(H,26,27)
InChIKeyIYODICUSAICAQL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCN(CCC)Cc1cc(ccc1N2C(=O)CCC2(CO)CO)C(=O)O
CACTVS 3.352CCCN(CCC)Cc1cc(ccc1N2C(=O)CCC2(CO)CO)C(O)=O
FormulaC20 H30 N2 O5
Name4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(dipropylamino)methyl]benzoic acid
ChEMBL
DrugBank
ZINCZINC000095921229
PDB chain4dgr Chain A Residue 488 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dgr Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking sub-site C6.
Resolution1.551 Å
Binding residue
(original residue number in PDB)		R118 E119 D151 R152 W178 I222 R224 E227 E277 R292 R371 Y406
Binding residue
(residue number reindexed from 1)		R38 E39 D71 R72 W99 I143 R145 E148 E198 R213 R291 Y325
Annotation score1
Binding affinityMOAD: ic50=9.1uM
PDBbind-CN: -logKd/Ki=5.04,IC50=9.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 E277 R292 R371 Y406
Catalytic site (residue number reindexed from 1) D71 E198 R213 R291 Y325
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
GO:0046761 viral budding from plasma membrane
Cellular Component
GO:0016020 membrane
GO:0033644 host cell membrane
GO:0055036 virion membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dgr, PDBe:4dgr, PDBj:4dgr
PDBsum4dgr
PubMed22559154
UniProtP03472|NRAM_I75A5 Neuraminidase (Gene Name=NA)

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