Structure of PDB 6dyy Chain C Binding Site BS01

Receptor Information
>6dyy Chain C (length=230) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYS
KIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQH
DVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASG
DQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNA
DEKAGMSFDEFLEKSAHTSAKFLKSMVDEL
Ligand information
Ligand IDOS6
InChIInChI=1S/C21H32N8OS/c1-2-3-6-29-11-17(26-27-29)5-4-7-31-13-16-10-28(12-18(16)30)9-15-8-23-20-19(15)24-14-25-21(20)22/h8,11,14,16,18,23,30H,2-7,9-10,12-13H2,1H3,(H2,22,24,25)/t16-,18+/m1/s1
InChIKeyRDPUFRZNTDIFPO-AEFFLSMTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCn1cc(nn1)CCCSC[C@H]2CN(C[C@@H]2O)Cc3c[nH]c4c3ncnc4N
CACTVS 3.385CCCCn1cc(CCCSC[CH]2CN(C[CH]2O)Cc3c[nH]c4c(N)ncnc34)nn1
CACTVS 3.385CCCCn1cc(CCCSC[C@H]2CN(C[C@@H]2O)Cc3c[nH]c4c(N)ncnc34)nn1
OpenEye OEToolkits 2.0.6CCCCn1cc(nn1)CCCSCC2CN(CC2O)Cc3c[nH]c4c3ncnc4N
ACDLabs 12.01OC1C(CN(C1)Cc3c2ncnc(N)c2nc3)CSCCCc4cn(nn4)CCCC
FormulaC21 H32 N8 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol
ChEMBLCHEMBL4450105
DrugBank
ZINC
PDB chain6dyy Chain C Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dyy Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		I52 A79 G80 F153 V154 E173 M174 E175 D198 F208
Binding residue
(residue number reindexed from 1)		I52 A79 G80 F153 V154 E173 M174 E175 D198 F208
Annotation score1
Binding affinityMOAD: Kd=0.028nM
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:6dyy, PDBe:6dyy, PDBj:6dyy
PDBsum6dyy
PubMed30860833
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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