Structure of PDB 4wkp Chain B Binding Site BS02

Receptor Information
>4wkp Chain B (length=230) Species: 85963 (Helicobacter pylori J99) [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 ID3QA
InChIInChI=1S/C17H27N5O3S/c18-17-16-15(20-11-21-17)13(7-19-16)9-22-8-12(14(24)10-22)1-5-26-6-4-25-3-2-23/h7,11-12,14,19,23-24H,1-6,8-10H2,(H2,18,20,21)/t12-,14-/m0/s1
InChIKeyNLPFBCRTOQVKFZ-JSGCOSHPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1c(c2c([nH]1)c(ncn2)N)CN3CC(C(C3)O)CCSCCOCCO
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CCSCCOCCO)C3)c[nH]c12
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CCSCCOCCO)C3)c[nH]c12
ACDLabs 12.01OCCOCCSCCC3CN(Cc2cnc1c2ncnc1N)CC3O
OpenEye OEToolkits 1.9.2c1c(c2c([nH]1)c(ncn2)N)CN3C[C@@H]([C@H](C3)O)CCSCCOCCO
FormulaC17 H27 N5 O3 S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(2-{[2-(2-hydroxyethoxy)ethyl]sulfanyl}ethyl)pyrrolidin-3-ol;
2-(2-hydroxyethoxy)ethylthiomethyl-DADMe-Immucillin-A
ChEMBL
DrugBank
ZINCZINC000150297495
PDB chain4wkp Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4wkp New Antibiotic Candidates against Helicobacter pylori.
Resolution1.58 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 affinityPDBbind-CN: -logKd/Ki=9.55,Ki=0.28nM
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:4wkp, PDBe:4wkp, PDBj:4wkp
PDBsum4wkp
PubMed26494017
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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