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"tautomers_smiles": true }, "126": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "11", "HBD": "5", "HMDBs": "HMDB0030388", "InChI": "InChI=1S/C16H23N5O5S/c1-8(5-22)3-4-17-13-10-14(20-16(19-13)27-2)21(7-18-10)15-12(25)11(24)9(6-23)26-15/h3,7,9,11-12,15,22-25H,4-6H2,1-2H3,(H,17,19,20)/t9-,11-,12-,15-/m1/s1", "InChIKey": "QEWSGVMSLPHELX-SDBHATRESA-N", "RCSB_ligands": "", "TPSA": "171.08", "abbrev": "\u2260", "atoms": "27", "building_blocks": "", "chemical_types": "heavy atom,other,other", "comment": "", "degeneracy": "not applicable", "formula": "C16H23N5O5S", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria", "lc_elution_comment": "after m6A (Kellner 2014)", "lc_elution_time": "3,19 (Kellner 2014)", "lc_reference_article": "904", "log_P": "-0.4168", "mass_avg": 397.449, "mass_monoiso": 397.142, "mass_prot": 398.1498, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000002160A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine", "nature": "Natural", "product_ions": "266", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "375", "rna_types": "tRNA", "short_name": "ms2io6A", "smile": "CC(CO)=CCNc1nc(SC)nc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O", "tautomers_image": true, "tautomers_smiles": true }, "127": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "9", "HBD": "3", "HMDBs": "HMDB0004326", "InChI": "InChI=1S/C11H15N5O4/c1-19-8-7(18)5(2-17)20-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1", "InChIKey": "FPUGCISOLXNPPC-IOSLPCCCSA-N", "RCSB_ligands": "", "TPSA": "128.54", "abbrev": "\u028d", "atoms": "20", "building_blocks": "", "chemical_types": "methyl group", "comment": "", "degeneracy": "not applicable", "formula": "C11H15N5O4", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria,Eukaryota", "lc_elution_comment": "between A and m6A (Kellner 2014, Kellner 2014)", "lc_elution_time": "1,59 (Kellner 2014); 1,83 (Kellner 2014)", "lc_reference_article": "904,905,906", "log_P": "-0.7447", "mass_avg": 281.268, "mass_monoiso": 281.1124, "mass_prot": 282.1195, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000090A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "2'-O-methyladenosine", "nature": "Natural", "product_ions": "136", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "207", "rna_types": "rRNA,snRNA,snoRNA,tRNA", "short_name": "Am", "smile": "CO[C@H]1[C@H]([n]2cnc3c2ncnc3N)O[C@H](CO)[C@H]1O", "tautomers_image": true, "tautomers_smiles": true }, "128": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "8", "HBD": "3", "HMDBs": "HMDB0000195", "InChI": "InChI=1S/C11H14N4O5/c1-19-8-7(17)5(2-16)20-11(8)15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)/t5-,7-,8-,11-/m1/s1", "InChIKey": "HPHXOIULGYVAKW-IOSLPCCCSA-N", "RCSB_ligands": "", "TPSA": "122.49", "abbrev": "\u0428", "atoms": "20", "building_blocks": "", "chemical_types": "methyl group,other", "comment": "", "degeneracy": "not applicable", "formula": "C11H14N4O5", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-1.6148", "mass_avg": 282.253, "mass_monoiso": 282.0964, "mass_prot": 283.1042, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000909A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "2'-O-methylinosine", "nature": "Natural", "product_ions": "137", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "367", "rna_types": "", "short_name": "Im", "smile": "CO[C@H]1[C@H]([n]2cnc3c2nc[nH]c3=O)O[C@H](CO)[C@H]1O", "tautomers_image": true, "tautomers_smiles": true }, "129": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "8", "HBD": "5", "HMDBs": "HMDB0000884", "InChI": "InChI=1S/C11H17N3O6/c1-12-2-5-3-14(11(19)13-9(5)18)10-8(17)7(16)6(4-15)20-10/h3,6-8,10,12,15-17H,2,4H2,1H3,(H,13,18,19)/t6-,7-,8-,10-/m1/s1", "InChIKey": "ZXQHKBUIXRFZBV-FDDDBJFASA-N", "RCSB_ligands": "", "TPSA": "136.81", "abbrev": "{", "atoms": "20", "building_blocks": "", "chemical_types": "methyl group,other", "comment": "", "degeneracy": "not applicable", "formula": "C11H17N3O6", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria,Eukaryota", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-2.7416", "mass_avg": 287.269, "mass_monoiso": 287.1117, "mass_prot": 288.1195, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000511U", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "5-methylaminomethyluridine", "nature": "Natural", "product_ions": "156/239/257/125/209", "pubchem_id": null, "reference_moiety": "Uridine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "297", "rna_types": "tRNA", "short_name": "mnm5U", "smile": "CNCc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1", "tautomers_image": true, "tautomers_smiles": true }, "130": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "14", "HBD": "7", "HMDBs": "HMDB0041623", "InChI": "InChI=1S/C15H21N7O7/c1-5(24)7(16)13(27)21-15(28)20-11-8-12(18-3-17-11)22(4-19-8)14-10(26)9(25)6(2-23)29-14/h3-7,9-10,14,23-26H,2,16H2,1H3,(H2,17,18,20,21,27,28)/t5?,6-,7?,9-,10-,14-/m1/s1", "InChIKey": "OPPXXSJNEJKHJA-GQFURFNTSA-N", "RCSB_ligands": "", "TPSA": "217.97", "abbrev": "6", "atoms": "29", "building_blocks": "", "chemical_types": "aminoacyl group,other", "comment": "", "degeneracy": "not applicable", "formula": "C15H21N7O7", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria,Eukaryota", "lc_elution_comment": "between A and m6A (Kellner 2014)", "lc_elution_time": "1,62 (Kellner 2014)", "lc_reference_article": "904,905", "log_P": "-2.0418", "mass_avg": 411.37, "mass_monoiso": 412.1343, "mass_prot": 413.1421, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000062A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "N6-threonylcarbamoyladenosine", "nature": "Natural", "product_ions": "281", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "231", "rna_types": "tRNA", "short_name": "t6A", "smile": "CC(O)C(N)C(NC(Nc1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O)=O)=O", "tautomers_image": true, "tautomers_smiles": true }, "131": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "9", "HBD": "4", "HMDBs": "HMDB0000050", "InChI": "InChI=1S/C11H15N5O4/c1-4-15-6-9(12)13-3-14-10(6)16(4)11-8(19)7(18)5(2-17)20-11/h3,5,7-8,11,17-19H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1", "InChIKey": "RTGYRFMTJZYXPD-IOSLPCCCSA-N", "RCSB_ligands": "", "TPSA": "139.54", "abbrev": "\u00e2", "atoms": "20", "building_blocks": "", "chemical_types": "methyl group", "comment": "

\r\nThe methyltransferase Cfr making m8A, has only been found in\r\n Staphylococcus sciuri so far, but it has been investigated in E. coli by expression\r\n of Cfr from a plasmid coded gene. It methylates A2503 in E. coli 23S RNA to m8A.\r\n

\r\nAlso see: \r\nIdentification of 8-methyladenosine as the modification catalyzed by the\r\n radical SAM methyltransferase Cfr that confers antibiotic resistance in\r\n bacteria. Giessing AM, Jensen SS, Rasmussen A, Hansen LH, Gondela A, Long K, Vester B,\r\n Kirpekar F. RNA. 2009 Feb;15(2):327-36.
\r\n PMID: 19144912\r\n", "degeneracy": "not applicable", "formula": "C11H15N5O4", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-1.0904", "mass_avg": 281.268, "mass_monoiso": 281.1124, "mass_prot": 282.1202, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000008A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "8-methyladenosine", "nature": "Natural", "product_ions": "150", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "410", "rna_types": "rRNA", "short_name": "m8A", "smile": "Cc1nc2c(N)ncnc2[n]1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O", "tautomers_image": true, "tautomers_smiles": true }, "132": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "20", "HBD": "6", "HMDBs": "HMDB0001273", "InChI": "", "InChIKey": "", "RCSB_ligands": "", "TPSA": "366.7", "abbrev": "\u00a9", "atoms": "42", "building_blocks": "", "chemical_types": "methyl group", "comment": "wikipedia: The 5' cap is found on the 5' end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA via an unusual 5' to 5' triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vitro by a methyl transferase. It is referred to as a 7-methylguanosine cap, abbreviated m7G.\r\n\r\nMost properties, save the triphosphate linkage, are the same as any other 7-methylguanosine.", "degeneracy": "unspecified residue", "formula": "C16H23N5O17P3", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eukaryota", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-1.5702", "mass_avg": 650.298, "mass_monoiso": 455.0243, "mass_prot": null, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000079553N", "moiety_type": "nucleotide", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "N7-methyl-guanosine cap (cap 0)", "nature": "Natural", "product_ions": "", "pubchem_id": null, "reference_moiety": "Adenosine, Uridine, Cytidine, Guanosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "", "rna_types": "mRNA,snRNA", "short_name": "m7GpppN", "smile": "C[n+]1c[n]([C@@H]2O[C@H](COP([O-])(OP([O-])(OP([O-])(OC[C@H]3O[C@@H]%91[C@H](O)[C@@H]3O)=O)=O)=O)[C@@H](O)[C@H]2O)c2c1c(nc(N)[nH]2)=O.[*]%91", "tautomers_image": true, "tautomers_smiles": true }, "133": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "20", "HBD": "6", "HMDBs": "HMDB0001273", "InChI": "", "InChIKey": "", "RCSB_ligands": "", "TPSA": "352.71", "abbrev": "\u00ae", "atoms": "43", "building_blocks": "", "chemical_types": "methyl group", "comment": "As with the m7G cap, the m2,7G cap is indistinguishable from any other m7m2G apart from the triester linkage linking it to the rest of the RNA chain, and I'm putting it here separately just for orderliness purpose.", "degeneracy": "unspecified residue", "formula": "C17H25N5O17P3", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eukaryota", "lc_elution_comment": null, "lc_elution_time": null, "lc_reference_article": "", "log_P": "-1.6189", "mass_avg": 664.325, "mass_monoiso": 469.04, "mass_prot": null, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000279553N", "moiety_type": "nucleotide", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "N2,7-dimethylguanosine cap (cap DMG)", "nature": "Natural", "product_ions": null, "pubchem_id": null, "reference_moiety": "Adenosine, Uridine, Cytidine, Guanosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "", "rna_types": "", "short_name": "m2,7GpppN", "smile": "CNc1nc(=O)c2c([n](c[n+]2C)[C@@H]2O[C@H](COP([O-])(OP([O-])(OP([O-])(OC[C@H]3O[C@@H]%91[C@H](O)[C@@H]3O)=O)=O)=O)[C@@H](O)[C@H]2O)[nH]1.[*]%91", "tautomers_image": true, "tautomers_smiles": true }, "134": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "20", "HBD": "5", "HMDBs": "HMDB0001273", "InChI": "", "InChIKey": "", "RCSB_ligands": "", "TPSA": "343.92", "abbrev": "\u00b6", "atoms": "44", "building_blocks": "", "chemical_types": "methyl group", "comment": "m2,2,7G cap is joined to the main chain via a 5'-5' linkage. Apart from sn- and snoRNAs it was found is some human selenoprotein mRNAs.", "degeneracy": "unspecified residue", "formula": "C18H27N5O17P3", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eukaryota", "lc_elution_comment": null, "lc_elution_time": null, "lc_reference_article": "", "log_P": "-1.6676", "mass_avg": 678.352, "mass_monoiso": 483.0556, "mass_prot": null, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2002279553N", "moiety_type": "nucleotide", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "N2,N2,7-trimethylguanosine cap (cap TMG)", "nature": "Natural", "product_ions": null, "pubchem_id": null, "reference_moiety": "Adenosine, Uridine, Cytidine, Guanosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "", "rna_types": "snRNA,snoRNA", "short_name": "m2,2,7GpppN", "smile": "CN(C)c1nc(=O)c2c([n](c[n+]2C)[C@@H]2O[C@H](COP([O-])(OP([O-])(OP([O-])(OC[C@H]3O[C@@H]%91[C@H](O)[C@@H]3O)=O)=O)=O)[C@@H](O)[C@H]2O)[nH]1.[*]%91", "tautomers_image": true, "tautomers_smiles": true }, "135": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "13", "HBD": "2", "HMDBs": "HMDB0060500", "InChI": "", "InChIKey": "", "RCSB_ligands": "", "TPSA": "236.43", "abbrev": "\u00a7", "atoms": "23", "building_blocks": "", "chemical_types": "other", "comment": "See 'Modification and Editing of RNA', edited by Henri Grosjean; chapter 11.", "degeneracy": "unspecified residue", "formula": "C6H11O13P3", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eukaryota", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "0.7143", "mass_avg": 384.065, "mass_monoiso": 172.9405, "mass_prot": null, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000001553N", "moiety_type": "nucleotide", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "gamma-methyltriphosphate 5' cap", "nature": "Natural", "product_ions": "", "pubchem_id": null, "reference_moiety": "Adenosine, Uridine, Cytidine, Guanosine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "", "rna_types": "snRNA", "short_name": "mpppN", "smile": "COP([O-])(OP([O-])(OP([O-])(OC[C@H]1O[C@@H]%91[C@H](O)[C@@H]1O)=O)=O)=O.[*]%91", "tautomers_image": false, "tautomers_smiles": false }, "136": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "9", "HBD": "4", "HMDBs": "HMDB0000050", "InChI": "InChI=1S/C12H17N5O4/c1-4-14-10(13)7-11(15-4)17(5(2)16-7)12-9(20)8(19)6(3-18)21-12/h6,8-9,12,18-20H,3H2,1-2H3,(H2,13,14,15)/t6-,8-,9-,12-/m1/s1", "InChIKey": "FGMBEEFIKCGALL-WOUKDFQISA-N", "RCSB_ligands": "", "TPSA": "139.54", "abbrev": "\u00b1", "atoms": "21", "building_blocks": "", "chemical_types": "methyl group", "comment": "", "degeneracy": "not applicable", "formula": "C12H17N5O4", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Eubacteria", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-0.782", "mass_avg": 295.294, "mass_monoiso": 295.1281, "mass_prot": 296.1358, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000028A", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "2,8-dimethyladenosine", "nature": "Natural", "product_ions": "164", "pubchem_id": null, "reference_moiety": "Adenosine", "related_articles": "259", "related_nucleosides": "", "related_nucleotides": "371", "rna_types": "rRNA", "short_name": "m2,8A", "smile": "Cc1nc2c(N)nc(C)nc2[n]1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O", "tautomers_image": true, "tautomers_smiles": true }, "137": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "11", "HBD": "5", "HMDBs": "HMDB0000497", "InChI": "InChI=1S/C13H21N3O8/c14-6(12(21)22)1-3-15-8(18)2-4-16(13(15)23)11-10(20)9(19)7(5-17)24-11/h6-7,9-11,17,19-20H,1-5,14H2,(H,21,22)/t6?,7-,9-,10-,11-/m1/s1", "InChIKey": "VBRZFUQRBSFADN-JANFQQFMSA-N", "RCSB_ligands": "", "TPSA": "173.86", "abbrev": "\u00d0", "atoms": "24", "building_blocks": "", "chemical_types": "aminoacyl group", "comment": "", "degeneracy": "not applicable", "formula": "C13H21N3O8", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-2.5422", "mass_avg": 347.321, "mass_monoiso": 347.1329, "mass_prot": 348.1407, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000308U", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine", "nature": "Natural", "product_ions": "216", "pubchem_id": null, "reference_moiety": "Uridine", "related_articles": "304", "related_nucleosides": "", "related_nucleotides": "381", "rna_types": "tRNA", "short_name": "acp3D", "smile": "NC(CCN1C(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)CCC1=O)C(O)=O", "tautomers_image": true, "tautomers_smiles": true }, "138": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "10", "HBD": "6", "HMDBs": "HMDB0000767", "InChI": "InChI=1S/C13H19N3O8/c14-6(12(21)22)1-2-16-11(20)5(3-15-13(16)23)10-9(19)8(18)7(4-17)24-10/h3,6-10,17-19H,1-2,4,14H2,(H,15,23)(H,21,22)/t6?,7-,8-,9-,10+/m1/s1", "InChIKey": "ZHENYVBBFCVMEV-BKLVVQOLSA-N", "RCSB_ligands": "", "TPSA": "188.1", "abbrev": "\u00de", "atoms": "24", "building_blocks": "", "chemical_types": "", "comment": "acp3Y is accumulated when the Nep1 enzyme is absent. The enzyme catalyzing the acp3Y formation in S. cerevisiae is still unknown.", "degeneracy": "not applicable", "formula": "C13H19N3O8", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-2.8071", "mass_avg": 345.305, "mass_monoiso": 345.1172, "mass_prot": 346.125, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000309U", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "3-(3-amino-3-carboxypropyl)pseudouridine", "nature": "Natural", "product_ions": "214", "pubchem_id": null, "reference_moiety": "Uridine", "related_articles": "305", "related_nucleosides": "", "related_nucleotides": "348", "rna_types": "", "short_name": "acp3Y", "smile": "NC(C(=O)O)CC[n]1c(=O)c([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c[nH]c1=O", "tautomers_image": true, "tautomers_smiles": true }, "139": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "10", "HBD": "3", "HMDBs": "HMDB0003950", "InChI": "InChI=1S/C14H17N5O5/c1-6-3-18-12(23)8-11(17(2)14(18)16-6)19(5-15-8)13-10(22)9(21)7(4-20)24-13/h3,5,7,9-10,13,20-22H,4H2,1-2H3/t7-,9-,10-,13-/m1/s1", "InChIKey": "JCZSFCLRSONYLH-QYVSTXNMSA-N", "RCSB_ligands": "", "TPSA": "127.04", "abbrev": "\u20ac", "atoms": "24", "building_blocks": "", "chemical_types": "", "comment": "", "degeneracy": "not applicable", "formula": "C14H17N5O5", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-1.6974", "mass_avg": 335.315, "mass_monoiso": 335.123, "mass_prot": 336.1308, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000034G", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "wyosine", "nature": "Natural", "product_ions": "204", "pubchem_id": null, "reference_moiety": "Guanosine", "related_articles": "306", "related_nucleosides": "", "related_nucleotides": "426", "rna_types": "", "short_name": "imG", "smile": "C[n]1c2c(nc[n]2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[n]2cc(C)nc12", "tautomers_image": false, "tautomers_smiles": false }, "140": { "CYP2C9_isoform_image": false, "CYP2D6_isoform_image": false, "CYP3A4_isoform_image": false, "HBA1": null, "HBD": null, "HMDBs": "", "InChI": null, "InChIKey": null, "RCSB_ligands": "", "TPSA": null, "abbrev": ".", "atoms": null, "building_blocks": "", "chemical_types": "", "comment": "", "degeneracy": "unspecified residue", "formula": "", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": null, "mass_avg": 0.0, "mass_monoiso": 0.0, "mass_prot": null, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": false, "modomics_code": "2000000000N", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "any ribonucleoside residue", "nature": "Natural", "product_ions": "", "pubchem_id": null, "reference_moiety": "Adenosine, Cytidine, Guanosine, Uridine", "related_articles": "", "related_nucleosides": "", "related_nucleotides": "", "rna_types": "tRNA", "short_name": "N", "smile": "", "tautomers_image": false, "tautomers_smiles": false }, "141": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "11", "HBD": "8", "HMDBs": "HMDB0003331", "InChI": "InChI=1S/C14H25N7O4/c15-9-3-6-21(12-11(24)10(23)8(7-22)25-12)14(20-9)19-5-2-1-4-18-13(16)17/h3,6,8,10-12,22-24H,1-2,4-5,7H2,(H2,15,19,20)(H4,16,17,18)/t8-,10-,11-,12-/m1/s1", "InChIKey": "NHQSDCRALZPVAJ-HJQYOEGKSA-N", "RCSB_ligands": "", "TPSA": "185.52", "abbrev": "\u00bf", "atoms": "25", "building_blocks": "", "chemical_types": "", "comment": "alternative name: 2-agmatinylcytidine, alternative abbreviation: agmt", "degeneracy": "not applicable", "formula": "C14H25N7O4", "in_DNA": "No", "in_RNA": "Yes", "kingdom_types": "Archaea", "lc_elution_comment": "", "lc_elution_time": "", "lc_reference_article": "", "log_P": "-0.9871", "mass_avg": 355.393, "mass_monoiso": 355.1968, "mass_prot": 356.2046, "modified_residue_2D_mol2_file": true, "modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000000020C", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "agmatidine", "nature": "Natural", "product_ions": "224", "pubchem_id": null, "reference_moiety": "Cytidine", "related_articles": "319,320,796", "related_nucleosides": "", "related_nucleotides": "411", "rna_types": 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"modified_residue_2D_mol_file": true, "modified_residue_2D_pdb_file": true, "modified_residue_2D_sdf_file": true, "modified_residue_2D_smi_file": true, "modified_residue_3D_mol2_file": true, "modified_residue_3D_mol_file": true, "modified_residue_3D_pdb_file": true, "modified_residue_3D_sdf_file": true, "modified_residue_image_file": true, "modomics_code": "2000009027G", "moiety_type": "nucleoside", "ms_file": false, "ms_reference": "", "msms_file": false, "msmsms_file": false, "name": "N2,7,2'-O-trimethylguanosine", "nature": "Natural", "product_ions": "180", "pubchem_id": null, "reference_moiety": "Guanosine", "related_articles": "809", "related_nucleosides": "", "related_nucleotides": "442", "rna_types": "", "short_name": "m2,7Gm", "smile": "[C@H]1([n]2c[n+](C)c3c2nc(nc3=O)NC)[C@H](OC)[C@H](O)[C@@H](CO)O1", "tautomers_image": true, "tautomers_smiles": true }, "143": { "CYP2C9_isoform_image": true, "CYP2D6_isoform_image": true, "CYP3A4_isoform_image": true, "HBA1": "9", "HBD": "5", 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Their identities were determined by mass spectrometry and confirmed by chemical synthesis. Data were presented at the tRNA meeting in Banz, Germany (1985) by P.F. Crain, D.R. Phillips, T. Hashizume and F. Widdel. 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