data_5EJ # _chem_comp.id 5EJ _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H19 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-09-16 _chem_comp.pdbx_modified_date 2016-08-05 _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 350.262 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5EJ _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 5DQG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 5EJ C1 C1 C 0 1 N N N -139.604 0.238 -7.821 5.337 1.980 1.034 C1 5EJ 1 5EJ C2 C2 C 0 1 N N N -139.124 4.971 -7.134 1.906 -0.023 0.574 C2 5EJ 2 5EJ P P1 P 0 1 N N N -132.742 6.179 -10.530 -4.632 1.384 -0.228 P 5EJ 3 5EJ OP1 O1 O 0 1 N N N -132.193 4.856 -10.129 -4.201 2.316 0.838 OP1 5EJ 4 5EJ "O5'" O2 O 0 1 N N N -133.565 6.934 -9.380 -3.469 0.303 -0.497 "O5'" 5EJ 5 5EJ "C5'" C3 C 0 1 N N N -134.709 7.762 -9.650 -2.914 -0.516 0.534 "C5'" 5EJ 6 5EJ "C4'" C4 C 0 1 N N R -135.639 7.859 -8.449 -1.838 -1.426 -0.062 "C4'" 5EJ 7 5EJ "C3'" C5 C 0 1 N N S -134.999 7.525 -7.118 -1.311 -2.407 1.008 "C3'" 5EJ 8 5EJ "O3'" O3 O 0 1 N N N -135.294 8.554 -6.197 -1.947 -3.680 0.877 "O3'" 5EJ 9 5EJ "C2'" C6 C 0 1 N N N -135.625 6.235 -6.645 0.199 -2.522 0.701 "C2'" 5EJ 10 5EJ "C1'" C7 C 0 1 N N R -136.994 6.353 -7.266 0.406 -1.597 -0.518 "C1'" 5EJ 11 5EJ "O4'" O4 O 0 1 N N N -136.718 6.943 -8.549 -0.683 -0.651 -0.452 "O4'" 5EJ 12 5EJ N1 N1 N 0 1 N N N -137.722 5.079 -7.447 1.693 -0.904 -0.421 N1 5EJ 13 5EJ C6 C8 C 0 1 N N N -137.072 4.026 -7.961 2.668 -1.154 -1.337 C6 5EJ 14 5EJ C5 C9 C 0 1 N N N -137.711 2.816 -8.193 3.855 -0.506 -1.235 C5 5EJ 15 5EJ C7 C10 C 0 1 N N N -136.881 1.674 -8.763 4.953 -0.762 -2.235 C7 5EJ 16 5EJ C4 C11 C 0 1 N N N -139.171 2.730 -7.845 4.044 0.408 -0.183 C4 5EJ 17 5EJ N3 N2 N 0 1 N N N -139.798 3.828 -7.342 3.066 0.624 0.683 N3 5EJ 18 5EJ O2 O5 O 0 1 N N N -139.745 5.927 -6.646 1.021 0.189 1.387 O2 5EJ 19 5EJ O4 O6 O 0 1 N N N -139.959 1.617 -8.031 5.218 1.067 -0.059 O4 5EJ 20 5EJ OP2 O7 O 0 1 N N N -131.700 7.045 -11.119 -5.974 0.625 0.233 OP2 5EJ 21 5EJ C3 C12 C 0 1 N N N -140.343 -0.704 -8.762 6.724 2.625 1.010 C3 5EJ 22 5EJ H1 H1 H 0 1 N N N -139.849 -0.035 -6.784 4.575 2.754 0.946 H1 5EJ 23 5EJ H2 H2 H 0 1 N N N -138.522 0.123 -7.985 5.203 1.442 1.973 H2 5EJ 24 5EJ H4 H4 H 0 1 N N N -134.362 8.772 -9.913 -2.470 0.118 1.301 H4 5EJ 25 5EJ H5 H5 H 0 1 N N N -135.266 7.334 -10.496 -3.701 -1.125 0.977 H5 5EJ 26 5EJ H6 H6 H 0 1 N N N -136.030 8.886 -8.398 -2.236 -1.973 -0.916 H6 5EJ 27 5EJ H7 H7 H 0 1 N N N -133.914 7.394 -7.244 -1.467 -2.002 2.008 H7 5EJ 28 5EJ H8 H8 H 0 1 N N N -134.896 8.353 -5.358 -1.653 -4.335 1.525 H8 5EJ 29 5EJ H9 H9 H 0 1 N N N -135.679 6.188 -5.547 0.789 -2.174 1.549 H9 5EJ 30 5EJ H10 H10 H 0 1 N N N -135.081 5.357 -7.023 0.461 -3.551 0.451 H10 5EJ 31 5EJ H11 H11 H 0 1 N N N -137.604 7.040 -6.661 0.354 -2.171 -1.443 H11 5EJ 32 5EJ H12 H12 H 0 1 N N N -136.023 4.121 -8.201 2.499 -1.861 -2.136 H12 5EJ 33 5EJ H13 H13 H 0 1 N N N -137.518 0.786 -8.892 4.856 -0.066 -3.068 H13 5EJ 34 5EJ H14 H14 H 0 1 N N N -136.467 1.973 -9.737 5.922 -0.619 -1.754 H14 5EJ 35 5EJ H15 H15 H 0 1 N N N -136.059 1.438 -8.072 4.878 -1.784 -2.604 H15 5EJ 36 5EJ H16 H16 H 0 1 N N N -130.870 6.582 -11.127 -6.314 -0.003 -0.419 H16 5EJ 37 5EJ H17 H17 H 0 1 N N N -140.036 -1.741 -8.560 7.487 1.851 1.099 H17 5EJ 38 5EJ H18 H18 H 0 1 N N N -141.427 -0.605 -8.603 6.859 3.163 0.072 H18 5EJ 39 5EJ H19 H19 H 0 1 N N N -140.100 -0.446 -9.804 6.815 3.322 1.844 H19 5EJ 40 5EJ OP3 OP3 O 0 1 N Y N -133.915 5.953 -11.739 -4.919 2.211 -1.579 OP3 5EJ 41 5EJ H3 H3 H 0 1 N Y N -133.999 5.026 -11.930 -5.610 2.882 -1.490 H3 5EJ 42 # 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 5EJ OP2 P SING N N 1 5EJ P OP1 DOUB N N 2 5EJ P "O5'" SING N N 3 5EJ "C5'" "O5'" SING N N 4 5EJ "C5'" "C4'" SING N N 5 5EJ C7 C5 SING N N 6 5EJ C3 C1 SING N N 7 5EJ "O4'" "C4'" SING N N 8 5EJ "O4'" "C1'" SING N N 9 5EJ "C4'" "C3'" SING N N 10 5EJ C5 C6 DOUB N N 11 5EJ C5 C4 SING N N 12 5EJ O4 C4 SING N N 13 5EJ O4 C1 SING N N 14 5EJ C6 N1 SING N N 15 5EJ C4 N3 DOUB N N 16 5EJ N1 "C1'" SING N N 17 5EJ N1 C2 SING N N 18 5EJ N3 C2 SING N N 19 5EJ "C1'" "C2'" SING N N 20 5EJ C2 O2 DOUB N N 21 5EJ "C3'" "C2'" SING N N 22 5EJ "C3'" "O3'" SING N N 23 5EJ C1 H1 SING N N 24 5EJ C1 H2 SING N N 25 5EJ "C5'" H4 SING N N 26 5EJ "C5'" H5 SING N N 27 5EJ "C4'" H6 SING N N 28 5EJ "C3'" H7 SING N N 29 5EJ "O3'" H8 SING N N 30 5EJ "C2'" H9 SING N N 31 5EJ "C2'" H10 SING N N 32 5EJ "C1'" H11 SING N N 33 5EJ C6 H12 SING N N 34 5EJ C7 H13 SING N N 35 5EJ C7 H14 SING N N 36 5EJ C7 H15 SING N N 37 5EJ OP2 H16 SING N N 38 5EJ C3 H17 SING N N 39 5EJ C3 H18 SING N N 40 5EJ C3 H19 SING N N 41 5EJ P OP3 SING N N 42 5EJ OP3 H3 SING N N 43 # 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 5EJ SMILES ACDLabs 12.01 "C(OC=1C(=CN(C(=O)N=1)C2CC(C(COP(=O)(O)O)O2)O)C)C" 5EJ InChI InChI 1.03 "InChI=1S/C12H19N2O8P/c1-3-20-11-7(2)5-14(12(16)13-11)10-4-8(15)9(22-10)6-21-23(17,18)19/h5,8-10,15H,3-4,6H2,1-2H3,(H2,17,18,19)/t8-,9+,10+/m0/s1" 5EJ InChIKey InChI 1.03 CNSVITKBNLMDOG-IVZWLZJFSA-N 5EJ SMILES_CANONICAL CACTVS 3.385 "CCOC1=NC(=O)N(C=C1C)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 5EJ SMILES CACTVS 3.385 "CCOC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 5EJ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CCOC1=NC(=O)N(C=C1C)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 5EJ SMILES "OpenEye OEToolkits" 1.9.2 "CCOC1=NC(=O)N(C=C1C)C2CC(C(O2)COP(=O)(O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 5EJ "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1H)-one" 5EJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(4-ethoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-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 5EJ "Create component" 2015-09-16 RCSB 5EJ "Initial release" 2016-08-10 RCSB #