data_E3C # _chem_comp.id E3C _chem_comp.name "3-ethyl, cytidine-5'-monophosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H20 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 2019-05-02 _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 353.266 _chem_comp.one_letter_code C _chem_comp.three_letter_code E3C _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 E3C "C1'" C1 C 0 1 N N R 346.635 180.376 284.820 -0.801 -1.000 0.331 "C1'" E3C 1 E3C C2 C2 C 0 1 N N N 345.850 182.031 286.654 -2.989 -0.025 0.585 C2 E3C 2 E3C "C2'" C3 C 0 1 N N R 345.526 179.336 284.647 -0.520 -2.066 -0.758 "C2'" E3C 3 E3C "C3'" C4 C 0 1 N N S 344.478 180.150 283.904 0.931 -2.492 -0.429 "C3'" E3C 4 E3C C4 C5 C 0 1 N N S 346.773 181.673 288.858 -3.815 1.671 -0.935 C4 E3C 5 E3C "C4'" C6 C 0 1 N N R 345.349 180.971 282.975 1.492 -1.317 0.394 "C4'" E3C 6 E3C C5 C7 C 0 1 N N N 347.481 180.600 288.363 -2.498 1.568 -1.675 C5 E3C 7 E3C "C5'" C8 C 0 1 N N N 344.722 182.159 282.289 2.731 -0.739 -0.293 "C5'" E3C 8 E3C C6 C9 C 0 1 N N N 347.384 180.258 287.032 -1.598 0.712 -1.226 C6 E3C 9 E3C N1 N1 N 0 1 N N N 346.622 180.943 286.186 -1.845 -0.072 -0.111 N1 E3C 10 E3C N3 N2 N 0 1 N N N 345.939 182.431 288.000 -3.996 0.802 0.240 N3 E3C 11 E3C N4 N3 N 0 1 N N N 346.947 181.915 290.167 -4.893 1.373 -1.888 N4 E3C 12 E3C O2 O1 O 0 1 N N N 345.103 182.695 285.909 -3.125 -0.753 1.550 O2 E3C 13 E3C "O2'" O2 O 0 1 N N N 346.019 178.287 283.828 -1.418 -3.171 -0.634 "O2'" E3C 14 E3C "O3'" O3 O 0 1 N N N 343.507 179.364 283.239 0.936 -3.695 0.342 "O3'" E3C 15 E3C "O4'" O4 O 0 1 N N N 346.440 181.376 283.838 0.463 -0.315 0.471 "O4'" E3C 16 E3C "O5'" O5 O 0 1 N N N 343.900 182.930 283.145 3.302 0.279 0.531 "O5'" E3C 17 E3C OP1 O6 O 0 1 N N N 342.403 184.881 283.682 5.722 0.161 -0.176 OP1 E3C 18 E3C OP2 O7 O 0 1 N N N 342.267 183.676 281.378 4.311 1.992 -1.189 OP2 E3C 19 E3C P P1 P 0 1 N N N 343.088 184.162 282.547 4.621 1.105 0.118 P E3C 20 E3C C31 C10 C 0 1 N N N 345.098 183.579 288.404 -5.239 0.836 1.014 C31 E3C 21 E3C C32 C11 C 0 1 N N N 345.708 184.760 289.131 -5.116 1.876 2.130 C32 E3C 22 E3C H1 H1 H 0 1 N N N 347.601 179.877 284.653 -1.084 -1.476 1.270 H1 E3C 23 E3C H2 H2 H 0 1 N N N 345.150 178.985 285.619 -0.581 -1.628 -1.755 H2 E3C 24 E3C H3 H3 H 0 1 N N N 343.989 180.828 284.619 1.507 -2.625 -1.345 H3 E3C 25 E3C H4 H4 H 0 1 N N N 345.929 181.008 289.093 -3.936 2.704 -0.610 H4 E3C 26 E3C H5 H5 H 0 1 N N N 345.743 180.299 282.198 1.749 -1.662 1.396 H5 E3C 27 E3C H6 H6 H 0 1 N N N 348.115 180.024 289.021 -2.300 2.177 -2.545 H6 E3C 28 E3C H7 H7 H 0 1 N N N 345.525 182.803 281.903 3.463 -1.532 -0.451 H7 E3C 29 E3C H8 H8 H 0 1 N N N 344.109 181.795 281.451 2.447 -0.311 -1.255 H8 E3C 30 E3C H9 H9 H 0 1 N N N 347.943 179.409 286.666 -0.651 0.622 -1.738 H9 E3C 31 E3C H10 H10 H 0 1 N N N 347.581 181.243 290.549 -4.849 1.987 -2.688 H10 E3C 32 E3C H11 H11 H 0 1 N N N 347.322 182.834 290.289 -4.866 0.405 -2.173 H11 E3C 33 E3C H13 H13 H 0 1 N N N 346.671 177.790 284.308 -1.282 -3.864 -1.294 H13 E3C 34 E3C H14 H14 H 0 1 N N N 343.000 178.878 283.879 0.541 -4.453 -0.109 H14 E3C 35 E3C H16 H16 H 0 1 N N N 341.354 183.902 281.516 3.598 2.634 -1.069 H16 E3C 36 E3C H17 H17 H 0 1 N N N 344.643 183.976 287.484 -6.068 1.103 0.359 H17 E3C 37 E3C H18 H18 H 0 1 N N N 344.311 183.178 289.059 -5.422 -0.145 1.451 H18 E3C 38 E3C H19 H19 H 0 1 N N N 344.926 185.504 289.343 -4.287 1.610 2.785 H19 E3C 39 E3C H20 H20 H 0 1 N N N 346.154 184.418 290.076 -4.934 2.858 1.693 H20 E3C 40 E3C H21 H21 H 0 1 N N N 346.487 185.215 288.502 -6.041 1.901 2.706 H21 E3C 41 E3C OP3 OP3 O 0 1 N N N 344.232 185.132 281.974 5.052 2.071 1.332 OP3 E3C 42 E3C H12 H12 H 0 1 N N N 344.235 185.945 282.466 5.841 2.600 1.152 H12 E3C 43 # # 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 E3C OP2 P SING N N 1 E3C "C5'" "C4'" SING N N 2 E3C "C5'" "O5'" SING N N 3 E3C P "O5'" SING N N 4 E3C P OP1 DOUB N N 5 E3C "C4'" "O4'" SING N N 6 E3C "C4'" "C3'" SING N N 7 E3C "O3'" "C3'" SING N N 8 E3C "O2'" "C2'" SING N N 9 E3C "O4'" "C1'" SING N N 10 E3C "C3'" "C2'" SING N N 11 E3C "C2'" "C1'" SING N N 12 E3C "C1'" N1 SING N N 13 E3C O2 C2 DOUB N N 14 E3C N1 C2 SING N N 15 E3C N1 C6 SING N N 16 E3C C2 N3 SING N N 17 E3C C6 C5 DOUB N N 18 E3C N3 C31 SING N N 19 E3C N3 C4 SING N N 20 E3C C5 C4 SING N N 21 E3C C31 C32 SING N N 22 E3C C4 N4 SING N N 23 E3C "C1'" H1 SING N N 24 E3C "C2'" H2 SING N N 25 E3C "C3'" H3 SING N N 26 E3C C4 H4 SING N N 27 E3C "C4'" H5 SING N N 28 E3C C5 H6 SING N N 29 E3C "C5'" H7 SING N N 30 E3C "C5'" H8 SING N N 31 E3C C6 H9 SING N N 32 E3C N4 H10 SING N N 33 E3C N4 H11 SING N N 34 E3C "O2'" H13 SING N N 35 E3C "O3'" H14 SING N N 36 E3C OP2 H16 SING N N 37 E3C C31 H17 SING N N 38 E3C C31 H18 SING N N 39 E3C C32 H19 SING N N 40 E3C C32 H20 SING N N 41 E3C C32 H21 SING N N 42 E3C P OP3 SING N N 43 E3C OP3 H12 SING N N 44 # # 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 E3C InChI InChI 1.03 "InChI=1S/C11H20N3O8P/c1-2-13-7(12)3-4-14(11(13)17)10-9(16)8(15)6(22-10)5-21-23(18,19)20/h3-4,6-10,15-16H,2,5,12H2,1H3,(H2,18,19,20)/t6-,7?,8-,9-,10-/m1/s1" E3C InChIKey InChI 1.03 PFBPABKTMDMXDL-HXURKHJASA-N E3C SMILES_CANONICAL CACTVS 3.385 "CCN1[C@H](N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O" E3C SMILES CACTVS 3.385 "CCN1[CH](N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O" E3C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N" E3C SMILES "OpenEye OEToolkits" 2.0.6 "CCN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id E3C _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-ethyl-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 E3C "Create component" 2017-09-25 EBI E3C "Initial release" 2018-01-24 RCSB E3C "Modify one letter code" 2019-05-02 EBI ##