Structure of PDB 3dp9 Chain A Binding Site BS01

Receptor Information
>3dp9 Chain A (length=229) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIG
KVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDAD
VTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDA
FVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVAD
KESPLSFEEFLPLAAKSSSAMVLKMVELL
Ligand information
Ligand IDBIG
InChIInChI=1S/C16H25N5OS/c1-2-3-4-23-9-12-7-21(8-13(12)22)6-11-5-18-15-14(11)19-10-20-16(15)17/h5,10,12-13,18,22H,2-4,6-9H2,1H3,(H2,17,19,20)/t12-,13+/m1/s1
InChIKeyLTSUEVPGSXUJHT-OLZOCXBDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
OpenEye OEToolkits 1.5.0CCCCSC[C@H]1C[N@](C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.341CCCCSC[CH]1CN(C[CH]1O)Cc2c[nH]c3c(N)ncnc23
CACTVS 3.341CCCCSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c(N)ncnc23
ACDLabs 10.04S(CCCC)CC3CN(Cc2cnc1c2ncnc1N)CC3O
FormulaC16 H25 N5 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol;
butylthio-DADMe-Immucillin A
ChEMBLCHEMBL1231347
DrugBankDB07463
ZINCZINC000013648011
PDB chain3dp9 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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PDB3dp9 Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I50 S76 A77 G78 F152 V153 V172 E173 M174 E175 D198 F208
Binding residue
(residue number reindexed from 1)		I49 S75 A76 G77 F151 V152 V171 E172 M173 E174 D197 F207
Annotation score1
Binding affinityMOAD: Kd=208pM
PDBbind-CN: -logKd/Ki=9.68,Kd=208pM
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:3dp9, PDBe:3dp9, PDBj:3dp9
PDBsum3dp9
PubMed19270684
UniProtQ9KPI8|MTNN_VIBCH 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (Gene Name=mtnN)

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