data_B8Q # _chem_comp.id B8Q _chem_comp.name "3-methyl, cytidine-5'-monophosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H18 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-25 _chem_comp.pdbx_modified_date 2019-04-29 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 339.239 _chem_comp.one_letter_code C _chem_comp.three_letter_code B8Q _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6EK0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal B8Q N1 N1 N 0 1 N N N 226.264 348.521 210.046 -2.066 -0.108 -0.091 N1 B8Q 1 B8Q C2 C1 C 0 1 N N N 225.534 347.355 210.346 -3.192 -0.093 -0.817 C2 B8Q 2 B8Q C5 C2 C 0 1 N N N 227.937 347.194 209.016 -2.713 -1.949 1.235 C5 B8Q 3 B8Q "C1'" C3 C 0 1 N N R 225.718 349.834 210.464 -1.040 0.896 -0.379 "C1'" B8Q 4 B8Q "C2'" C4 C 0 1 N N R 225.969 350.127 211.940 -0.856 1.850 0.829 "C2'" B8Q 5 B8Q "C3'" C5 C 0 1 N N S 227.219 350.985 211.851 0.592 2.359 0.623 "C3'" B8Q 6 B8Q C4 C6 C 0 1 N N S 227.246 346.031 209.288 -4.004 -1.995 0.445 C4 B8Q 7 B8Q "C4'" C7 C 0 1 N N R 226.922 351.825 210.631 1.239 1.297 -0.287 "C4'" B8Q 8 B8Q "C5'" C8 C 0 1 N N N 228.106 352.491 209.990 2.466 0.698 0.404 "C5'" B8Q 9 B8Q C6 C9 C 0 1 N N N 227.426 348.421 209.399 -1.826 -1.022 0.923 C6 B8Q 10 B8Q C31 C10 C 0 1 N N N 225.266 344.889 210.265 -5.401 -0.955 -1.424 C31 B8Q 11 B8Q N3 N2 N 0 1 N N N 226.027 346.102 209.966 -4.182 -0.985 -0.611 N3 B8Q 12 B8Q N4 N3 N 0 1 N N N 227.745 344.838 208.908 -5.118 -1.843 1.391 N4 B8Q 13 B8Q O2 O1 O 0 1 N N N 224.442 347.416 210.941 -3.324 0.747 -1.686 O2 B8Q 14 B8Q "O2'" O2 O 0 1 N N N 224.874 350.887 212.419 -1.789 2.931 0.772 "O2'" B8Q 15 B8Q "O3'" O3 O 0 1 N N N 227.506 351.738 213.012 0.587 3.634 -0.022 "O3'" B8Q 16 B8Q "O4'" O4 O 0 1 N N N 226.336 350.865 209.721 0.256 0.274 -0.516 "O4'" B8Q 17 B8Q "O5'" O5 O 0 1 N N N 229.263 351.687 210.124 3.126 -0.199 -0.491 "O5'" B8Q 18 B8Q OP1 O6 O 0 1 N N N 230.746 350.180 208.832 4.216 -1.783 1.144 OP1 B8Q 19 B8Q OP2 O7 O 0 1 N N N 231.401 352.667 209.257 4.850 -2.017 -1.288 OP2 B8Q 20 B8Q P P1 P 0 1 N N N 230.358 351.624 208.978 4.459 -1.010 -0.095 P B8Q 21 B8Q H1 H1 H 0 1 N N N 228.884 347.146 208.500 -2.519 -2.661 2.024 H1 B8Q 22 B8Q H2 H2 H 0 1 N N N 224.632 349.843 210.287 -1.296 1.459 -1.276 H2 B8Q 23 B8Q H3 H3 H 0 1 N N N 226.146 349.205 212.513 -0.948 1.309 1.770 H3 B8Q 24 B8Q H4 H4 H 0 1 N N N 228.070 350.328 211.618 1.115 2.417 1.577 H4 B8Q 25 B8Q H5 H5 H 0 1 N N N 226.718 346.118 208.327 -4.086 -2.983 -0.007 H5 B8Q 26 B8Q H6 H6 H 0 1 N N N 226.178 352.591 210.896 1.532 1.750 -1.234 H6 B8Q 27 B8Q H7 H7 H 0 1 N N N 228.282 353.462 210.477 3.150 1.498 0.687 H7 B8Q 28 B8Q H8 H8 H 0 1 N N N 227.897 352.649 208.922 2.152 0.156 1.296 H8 B8Q 29 B8Q H9 H9 H 0 1 N N N 227.981 349.319 209.169 -0.895 -0.975 1.469 H9 B8Q 30 B8Q H10 H10 H 0 1 N N N 224.343 345.157 210.800 -6.141 -0.313 -0.945 H10 B8Q 31 B8Q H11 H11 H 0 1 N N N 225.010 344.376 209.326 -5.167 -0.564 -2.414 H11 B8Q 32 B8Q H12 H12 H 0 1 N N N 225.873 344.221 210.894 -5.801 -1.965 -1.516 H12 B8Q 33 B8Q H13 H13 H 0 1 N N N 227.117 344.110 209.185 -5.115 -2.585 2.075 H13 B8Q 34 B8Q H14 H14 H 0 1 N N N 227.854 344.824 207.914 -5.092 -0.939 1.838 H14 B8Q 35 B8Q H16 H16 H 0 1 N N N 225.004 351.085 213.339 -1.714 3.556 1.506 H16 B8Q 36 B8Q H17 H17 H 0 1 N N N 227.682 351.149 213.736 0.139 4.328 0.482 H17 B8Q 37 B8Q H19 H19 H 0 1 N N N 232.255 352.255 209.313 5.645 -2.540 -1.118 H19 B8Q 38 B8Q OP3 OP3 O 0 1 N N N 229.558 352.050 207.656 5.666 0.027 0.149 OP3 B8Q 39 B8Q H15 H15 H 0 1 N N N 229.500 351.307 207.067 5.881 0.569 -0.623 H15 B8Q 40 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal B8Q OP1 P DOUB N N 1 B8Q N4 C4 SING N N 2 B8Q P OP2 SING N N 3 B8Q P "O5'" SING N N 4 B8Q C5 C4 SING N N 5 B8Q C5 C6 DOUB N N 6 B8Q C4 N3 SING N N 7 B8Q C6 N1 SING N N 8 B8Q "O4'" "C1'" SING N N 9 B8Q "O4'" "C4'" SING N N 10 B8Q N3 C31 SING N N 11 B8Q N3 C2 SING N N 12 B8Q "C5'" "O5'" SING N N 13 B8Q "C5'" "C4'" SING N N 14 B8Q N1 C2 SING N N 15 B8Q N1 "C1'" SING N N 16 B8Q C2 O2 DOUB N N 17 B8Q "C1'" "C2'" SING N N 18 B8Q "C4'" "C3'" SING N N 19 B8Q "C3'" "C2'" SING N N 20 B8Q "C3'" "O3'" SING N N 21 B8Q "C2'" "O2'" SING N N 22 B8Q C5 H1 SING N N 23 B8Q "C1'" H2 SING N N 24 B8Q "C2'" H3 SING N N 25 B8Q "C3'" H4 SING N N 26 B8Q C4 H5 SING N N 27 B8Q "C4'" H6 SING N N 28 B8Q "C5'" H7 SING N N 29 B8Q "C5'" H8 SING N N 30 B8Q C6 H9 SING N N 31 B8Q C31 H10 SING N N 32 B8Q C31 H11 SING N N 33 B8Q C31 H12 SING N N 34 B8Q N4 H13 SING N N 35 B8Q N4 H14 SING N N 36 B8Q "O2'" H16 SING N N 37 B8Q "O3'" H17 SING N N 38 B8Q OP2 H19 SING N N 39 B8Q P OP3 SING N N 40 B8Q OP3 H15 SING N N 41 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor B8Q InChI InChI 1.03 "InChI=1S/C10H18N3O8P/c1-12-6(11)2-3-13(10(12)16)9-8(15)7(14)5(21-9)4-20-22(17,18)19/h2-3,5-9,14-15H,4,11H2,1H3,(H2,17,18,19)/t5-,6+,7-,8-,9-/m1/s1" B8Q InChIKey InChI 1.03 HUUPYGHSEPUDJF-ANZWQOBJSA-N B8Q SMILES_CANONICAL CACTVS 3.385 "CN1[C@H](N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O" B8Q SMILES CACTVS 3.385 "CN1[CH](N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O" B8Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N" B8Q SMILES "OpenEye OEToolkits" 2.0.6 "CN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id B8Q _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site B8Q "Create component" 2017-09-25 EBI B8Q "Modify linking type" 2017-09-25 EBI B8Q "Modify one letter code" 2019-04-29 EBI ##