Structure of PDB 5kb3 Chain A Binding Site BS01

Receptor Information
>5kb3 Chain A (length=230) Species: 85963 (Helicobacter pylori J99) [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 ID4CT
InChIInChI=1S/C18H20ClN5OS/c19-13-1-3-14(4-2-13)26-9-12-7-24(8-15(12)25)6-11-5-21-17-16(11)22-10-23-18(17)20/h1-5,10,12,15,21,25H,6-9H2,(H2,20,22,23)/t12-,15+/m1/s1
InChIKeyMZZBHZOHYGEGEE-DOMZBBRYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2c(CN3C[CH](O)[CH](CSc4ccc(Cl)cc4)C3)c[nH]c12
OpenEye OEToolkits 1.7.0c1cc(ccc1SC[C@H]2C[N@](C[C@@H]2O)Cc3c[nH]c4c3ncnc4N)Cl
ACDLabs 12.01Clc4ccc(SCC3CN(Cc2cnc1c2ncnc1N)CC3O)cc4
OpenEye OEToolkits 1.7.0c1cc(ccc1SCC2CN(CC2O)Cc3c[nH]c4c3ncnc4N)Cl
CACTVS 3.370Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSc4ccc(Cl)cc4)C3)c[nH]c12
FormulaC18 H20 Cl N5 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol
ChEMBLCHEMBL1230265
DrugBank
ZINCZINC000011686335
PDB chain5kb3 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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PDB5kb3 Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states.
Resolution1.399 Å
Binding residue
(original residue number in PDB)		I52 A79 G80 F153 V154 E173 M174 E175 D198 A200 F208
Binding residue
(residue number reindexed from 1)		I52 A79 G80 F153 V154 E173 M174 E175 D198 A200 F208
Annotation score1
Binding affinityMOAD: Kd=570pM
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:5kb3, PDBe:5kb3, PDBj:5kb3
PDBsum5kb3
PubMed27856757
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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