Structure of PDB 4wkb Chain B Binding Site BS01

Receptor Information
>4wkb Chain B (length=237) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGI
GKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDA
DVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGD
AFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVA
DKESPLSFEEFLPLAAKSSSAMVLKMVELLKENLYFQ
Ligand information
Ligand IDTDI
InChIInChI=1S/C13H19N5OS/c1-20-6-9-4-18(5-10(9)19)3-8-2-15-12-11(8)16-7-17-13(12)14/h2,7,9-10,15,19H,3-6H2,1H3,(H2,14,16,17)/t9-,10+/m1/s1
InChIKeyNTHMDFGHOCNNOE-ZJUUUORDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.341CSC[CH]1CN(C[CH]1O)Cc2c[nH]c3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@H]1C[N@](C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.341CSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c(N)ncnc23
ACDLabs 10.04S(C)CC3CN(Cc2cnc1c2ncnc1N)CC3O
FormulaC13 H19 N5 O S
Name(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL;
(3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE
ChEMBLCHEMBL405346
DrugBankDB08606
ZINCZINC000011686540
PDB chain4wkb 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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PDB4wkb Active site and remote contributions to catalysis in methylthioadenosine nucleosidases.
Resolution1.37 Å
Binding residue
(original residue number in PDB)		I50 S76 A77 G78 F152 V153 E173 M174 E175 D198 F208
Binding residue
(residue number reindexed from 1)		I50 S76 A77 G78 F152 V153 E173 M174 E175 D198 F208
Annotation score1
Binding affinityMOAD: Ki=2.7pM
PDBbind-CN: -logKd/Ki=11.57,Ki=2.7pM
Enzymatic activity
Enzyme Commision number 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
Biological Process
GO:0009086 methionine biosynthetic process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic 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:4wkb, PDBe:4wkb, PDBj:4wkb
PDBsum4wkb
PubMed25806409
UniProtA5F5R2|MTNN_VIBC3 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (Gene Name=mtnN)

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