Structure of PDB 6dyv Chain B Binding Site BS01

Receptor Information
>6dyv Chain B (length=232) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGVQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVA
YSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLV
QHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIA
SGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISD
NADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL
Ligand information
Ligand IDOS3
InChIInChI=1S/C17H23N5OS/c1-2-3-4-5-24-10-13-8-22(9-14(13)23)7-12-6-19-16-15(12)20-11-21-17(16)18/h1,6,11,13-14,19,23H,3-5,7-10H2,(H2,18,20,21)/t13-,14+/m1/s1
InChIKeyQRFSYYUFBJRRLL-KGLIPLIRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CSCCCC#C)C3)c[nH]c12
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCC#C)C3)c[nH]c12
ACDLabs 12.01Nc1c2ncc(c2ncn1)CN3CC(O)C(C3)CSCCCC#C
OpenEye OEToolkits 2.0.6C#CCCCSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
OpenEye OEToolkits 2.0.6C#CCCCSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
FormulaC17 H23 N5 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol
ChEMBLCHEMBL4465346
DrugBank
ZINC
PDB chain6dyv Chain B Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dyv Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Resolution1.62 Å
Binding residue
(original residue number in PDB)		I52 V78 A79 G80 F153 V154 E173 M174 E175 D198 F208
Binding residue
(residue number reindexed from 1)		I54 V80 A81 G82 F155 V156 E175 M176 E177 D200 F210
Annotation score1
Binding affinityMOAD: Kd=0.026nM
PDBbind-CN: -logKd/Ki=10.59,Kd=0.026nM
Enzymatic activity
Enzyme Commision number 3.2.2.30: aminodeoxyfutalosine nucleosidase.
3.2.2.9: adenosylhomocysteine nucleosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008782 adenosylhomocysteine nucleosidase activity
GO:0008930 methylthioadenosine nucleosidase activity
GO:0016787 hydrolase activity
GO:0102246 6-amino-6-deoxyfutalosine hydrolase activity
Biological Process
GO:0009086 methionine biosynthetic process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
GO:0009234 menaquinone biosynthetic process
GO:0019284 L-methionine salvage from S-adenosylmethionine
GO:0019509 L-methionine salvage from methylthioadenosine
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6dyv, PDBe:6dyv, PDBj:6dyv
PDBsum6dyv
PubMed30860833
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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