Structure of PDB 3nm5 Chain B Binding Site BS01

Receptor Information
>3nm5 Chain B (length=229) Species: 85963 (Helicobacter pylori J99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSK
IGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHD
VDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGD
QFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNAD
EKAGMSFDEFLEKSAHTSAKFLKSMVDEL
Ligand information
Ligand IDFMC
InChIInChI=1S/C10H13N5O4/c11-10-6-4(12-2-13-10)5(14-15-6)9-8(18)7(17)3(1-16)19-9/h2-3,7-9,16-18H,1H2,(H,14,15)(H2,11,12,13)/t3-,7-,8-,9+/m1/s1
InChIKeyKBHMEHLJSZMEMI-KSYZLYKTSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2c1[nH]nc2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2c1[nH]nc2[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 12.01OC1C(OC(CO)C1O)c3nnc2c3ncnc2N
OpenEye OEToolkits 1.7.0c1nc2c(c(n1)N)[nH]nc2C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.7.0c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
FormulaC10 H13 N5 O4
Name(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
ChEMBLCHEMBL471524
DrugBankDB02281
ZINCZINC000018275505
PDB chain3nm5 Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nm5 Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		F153 V154 E173 M174 E175 D198 F208
Binding residue
(residue number reindexed from 1)		F152 V153 E172 M173 E174 D197 F207
Annotation score1
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:3nm5, PDBe:3nm5, PDBj:3nm5
PDBsum3nm5
PubMed20954236
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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