Structure of PDB 5cce Chain A Binding Site BS01

Receptor Information
>5cce Chain A (length=230) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYS
KIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQH
DVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASG
DQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNA
DEKAGMSFDEFLEKSAHTSAKFLKSMVDEL
Ligand information
Ligand ID2WP
InChIInChI=1S/C9H17NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3,10H2,(H,13,14)/t4-,5+,6+,7+,9-/m0/s1
InChIKeyIQFWYNFDWRYSRA-LYNCRYNASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(CSC[C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)[C@@H](C(=O)O)N
CACTVS 3.385N[CH](CCSC[CH]1O[CH](O)[CH](O)[CH]1O)C(O)=O
CACTVS 3.385N[C@@H](CCSC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O)C(O)=O
OpenEye OEToolkits 1.7.6C(CSCC1C(C(C(O1)O)O)O)C(C(=O)O)N
ACDLabs 12.01O=C(O)C(N)CCSCC1OC(O)C(O)C1O
FormulaC9 H17 N O6 S
NameS-ribosylhomocysteine;
(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid
ChEMBL
DrugBank
ZINCZINC000013544480
PDB chain5cce Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cce Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		M10 E13 I52 V78 F153 M174 E175 R194 F208
Binding residue
(residue number reindexed from 1)		M10 E13 I52 V78 F153 M174 E175 R194 F208
Annotation score5
Enzymatic activity
Enzyme Commision number 3.2.2.30: aminodeoxyfutalosine nucleosidase.
3.2.2.9: adenosylhomocysteine nucleosidase.
Gene Ontology
Molecular Function
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:0009234 menaquinone biosynthetic process
GO:0019284 L-methionine salvage from S-adenosylmethionine
GO:0019509 L-methionine salvage from methylthioadenosine
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5cce, PDBe:5cce, PDBj:5cce
PDBsum5cce
PubMed27856757
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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