Structure of PDB 1nc1 Chain A Binding Site BS01

Receptor Information
>1nc1 Chain A (length=234) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSMKIGIIGAMEEEVTLLRDKIENRQTISLGGCEIYTGQLNGTEVALLKS
GIGKVAAALGATLLLEHCKPDVIINTGSAGGLAPTLKVGDIVVSDEARYH
DADVTAFGYEYGQLPGCPAGFKADDKLIAAAEACIAELNLNAVRGLIVSG
DAFINGSVGLAKIRHNFPQAIAVEMEATAIAHVCHNFNVPFVVVRAISDV
ADQQSHLSFDEFLAVAAKQSSLMVESLVQKLAHG
Ligand information
Ligand IDMTH
InChIInChI=1S/C12H16N4O3S/c1-20-4-7-8(17)9(18)12(19-7)16-3-2-6-10(13)14-5-15-11(6)16/h2-3,5,7-9,12,17-18H,4H2,1H3,(H2,13,14,15)/t7-,8-,9-,12-/m1/s1
InChIKeyWBPLMFVTQMIPLW-MFYTUXHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2ccc3c2ncnc3N)O)O
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2ccc3c(N)ncnc23
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2ccc3c(N)ncnc23
ACDLabs 10.04S(C)CC3OC(n2ccc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2ccc3c2ncnc3N)O)O
FormulaC12 H16 N4 O3 S
Name2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL;
5'-DEOXY-5'-(METHYLTHIO)-TUBERCIDIN
ChEMBLCHEMBL551561
DrugBankDB02933
ZINCZINC000005141416
PDB chain1nc1 Chain A Residue 233 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nc1 Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		M9 I50 S76 A77 G78 F151 I152 E172 M173 E174 D197 F207
Binding residue
(residue number reindexed from 1)		M11 I52 S78 A79 G80 F153 I154 E174 M175 E176 D199 F209
Annotation score3
Binding affinityMOAD: Ki=0.75uM
PDBbind-CN: -logKd/Ki=6.12,Ki=0.75uM
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
GO:0042802 identical protein binding
GO:0042803 protein homodimerization 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
GO:0046124 purine deoxyribonucleoside catabolic process
GO:0110052 toxic metabolite repair
Cellular Component
GO:0005737 cytoplasm
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:1nc1, PDBe:1nc1, PDBj:1nc1
PDBsum1nc1
PubMed12496243
UniProtP0AF12|MTNN_ECOLI 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (Gene Name=mtnN)

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