data_EJ8 # _chem_comp.id EJ8 _chem_comp.name "[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H22 N2 O11 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-03-23 _chem_comp.pdbx_modified_date 2018-07-06 _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 536.387 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EJ8 _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 6G2L _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 EJ8 "C2'" C1 C 0 1 N N N -5.136 27.293 28.264 2.275 1.821 -0.960 "C2'" EJ8 1 EJ8 "C1'" C2 C 0 1 N N R -3.641 27.690 28.044 1.102 2.333 -1.827 "C1'" EJ8 2 EJ8 O2 O1 O 0 1 N N N -1.360 28.362 26.705 0.824 4.397 -0.141 O2 EJ8 3 EJ8 O9 O2 O 0 1 N N N -5.439 20.138 22.740 -3.188 -3.331 0.208 O9 EJ8 4 EJ8 P2 P1 P 0 1 N N N -4.118 20.029 23.349 -4.433 -2.443 -0.292 P2 EJ8 5 EJ8 O10 O3 O 0 1 N N N -2.966 20.641 22.682 -4.090 -1.791 -1.576 O10 EJ8 6 EJ8 O11 O4 O 0 1 N N N -3.910 18.769 24.140 -5.719 -3.389 -0.498 O11 EJ8 7 EJ8 C18 C3 C 0 1 N N N -4.345 21.139 24.807 -4.811 -1.168 0.955 C18 EJ8 8 EJ8 S1 S1 S 0 1 N N N -3.027 22.379 25.187 -3.362 -0.101 1.186 S1 EJ8 9 EJ8 C17 C4 C 0 1 N N N -3.934 23.899 24.718 -3.373 0.932 -0.305 C17 EJ8 10 EJ8 C5 C5 C 0 1 N N N -3.269 25.032 25.222 -2.210 1.889 -0.262 C5 EJ8 11 EJ8 C4 C6 C 0 1 N N N -3.755 25.721 26.313 -1.124 1.681 -1.037 C4 EJ8 12 EJ8 C6 C7 C 0 1 N N N -2.142 25.528 24.615 -2.243 3.021 0.587 C6 EJ8 13 EJ8 O6 O5 O 0 1 N N N -1.670 24.993 23.617 -3.213 3.232 1.292 O6 EJ8 14 EJ8 N1 N1 N 0 1 N N N -1.533 26.663 25.134 -1.190 3.863 0.609 N1 EJ8 15 EJ8 C8 C8 C 0 1 N N N -1.978 27.355 26.275 -0.118 3.628 -0.171 C8 EJ8 16 EJ8 N9 N2 N 0 1 N N N -3.090 26.909 26.859 -0.076 2.559 -0.986 N9 EJ8 17 EJ8 "O4'" O6 O 0 1 N N N -2.977 27.563 29.269 0.815 1.326 -2.805 "O4'" EJ8 18 EJ8 "C3'" C9 C 0 1 N N R -5.167 26.800 29.695 2.908 0.754 -1.882 "C3'" EJ8 19 EJ8 "O3'" O7 O 0 1 N N N -4.956 25.383 29.628 3.615 -0.221 -1.145 "O3'" EJ8 20 EJ8 "C4'" C10 C 0 1 N N R -3.972 27.518 30.314 1.661 0.176 -2.582 "C4'" EJ8 21 EJ8 "C5'" C11 C 0 1 N N N -3.341 26.820 31.455 0.908 -0.757 -1.627 "C5'" EJ8 22 EJ8 O7 O8 O 0 1 N N N -3.270 25.340 31.229 1.815 -1.673 -1.015 O7 EJ8 23 EJ8 CAB C12 C 0 1 N N R -4.485 24.724 30.827 2.835 -1.017 -0.252 CAB EJ8 24 EJ8 P P2 P 0 1 N N N -5.745 24.759 32.211 3.899 -2.260 0.552 P EJ8 25 EJ8 OP1 O9 O 0 1 N N N -6.202 26.147 32.530 4.559 -3.208 -0.570 OP1 EJ8 26 EJ8 OP2 O10 O 0 1 N N N -6.831 23.852 31.842 4.969 -1.577 1.312 OP2 EJ8 27 EJ8 OP3 O11 O 0 1 N N N -4.915 24.107 33.356 3.014 -3.154 1.557 OP3 EJ8 28 EJ8 C2 C13 C 0 1 Y N N -4.229 23.353 30.433 2.201 -0.136 0.793 C2 EJ8 29 EJ8 CAA C14 C 0 1 Y N N -4.940 22.753 29.388 0.848 -0.238 1.055 CAA EJ8 30 EJ8 C9 C15 C 0 1 Y N N -4.722 21.426 29.047 0.266 0.570 2.013 C9 EJ8 31 EJ8 C10 C16 C 0 1 Y N N -3.781 20.699 29.716 1.038 1.480 2.711 C10 EJ8 32 EJ8 C11 C17 C 0 1 Y N N -3.018 21.266 30.733 2.392 1.582 2.450 C11 EJ8 33 EJ8 C12 C18 C 0 1 Y N N -3.273 22.595 31.085 2.974 0.770 1.495 C12 EJ8 34 EJ8 H1 H1 H 0 1 N N N -5.797 28.163 28.134 2.983 2.623 -0.749 H1 EJ8 35 EJ8 H2 H2 H 0 1 N N N -5.437 26.497 27.568 1.911 1.372 -0.036 H2 EJ8 36 EJ8 H3 H3 H 0 1 N N N -3.640 28.752 27.756 1.387 3.261 -2.324 H3 EJ8 37 EJ8 H4 H4 H 0 1 N N N -5.375 20.629 21.929 -3.342 -3.788 1.046 H4 EJ8 38 EJ8 H5 H5 H 0 1 N N N -2.995 18.517 24.101 -5.590 -4.093 -1.149 H5 EJ8 39 EJ8 H6 H6 H 0 1 N N N -5.279 21.697 24.648 -5.654 -0.566 0.615 H6 EJ8 40 EJ8 H7 H7 H 0 1 N N N -4.449 20.495 25.692 -5.064 -1.648 1.900 H7 EJ8 41 EJ8 H8 H8 H 0 1 N N N -3.989 23.967 23.621 -3.289 0.297 -1.187 H8 EJ8 42 EJ8 H9 H9 H 0 1 N N N -4.951 23.859 25.134 -4.305 1.495 -0.350 H9 EJ8 43 EJ8 H10 H10 H 0 1 N N N -4.662 25.372 26.785 -1.082 0.824 -1.694 H10 EJ8 44 EJ8 H11 H11 H 0 1 N N N -0.722 27.012 24.664 -1.205 4.641 1.188 H11 EJ8 45 EJ8 H12 H12 H 0 1 N N N -6.107 27.071 30.199 3.559 1.232 -2.614 H12 EJ8 46 EJ8 H13 H13 H 0 1 N N N -4.269 28.535 30.610 1.921 -0.317 -3.519 H13 EJ8 47 EJ8 H14 H14 H 0 1 N N N -2.321 27.209 31.591 0.418 -0.164 -0.855 H14 EJ8 48 EJ8 H15 H15 H 0 1 N N N -3.932 27.014 32.362 0.157 -1.315 -2.185 H15 EJ8 49 EJ8 H16 H16 H 0 1 N N N -7.146 26.200 32.435 3.914 -3.688 -1.108 H16 EJ8 50 EJ8 H17 H17 H 0 1 N N N -5.286 23.260 33.574 3.516 -3.838 2.020 H17 EJ8 51 EJ8 H18 H18 H 0 1 N N N -5.669 23.331 28.839 0.244 -0.949 0.510 H18 EJ8 52 EJ8 H19 H19 H 0 1 N N N -5.296 20.970 28.254 -0.792 0.491 2.217 H19 EJ8 53 EJ8 H20 H20 H 0 1 N N N -3.625 19.664 29.451 0.583 2.112 3.460 H20 EJ8 54 EJ8 H21 H21 H 0 1 N N N -2.251 20.696 31.236 2.995 2.293 2.995 H21 EJ8 55 EJ8 H22 H22 H 0 1 N N N -2.707 23.043 31.889 4.032 0.847 1.294 H22 EJ8 56 # 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 EJ8 O10 P2 DOUB N N 1 EJ8 O9 P2 SING N N 2 EJ8 P2 O11 SING N N 3 EJ8 P2 C18 SING N N 4 EJ8 O6 C6 DOUB N N 5 EJ8 C6 N1 SING N N 6 EJ8 C6 C5 SING N N 7 EJ8 C17 S1 SING N N 8 EJ8 C17 C5 SING N N 9 EJ8 C18 S1 SING N N 10 EJ8 N1 C8 SING N N 11 EJ8 C5 C4 DOUB N N 12 EJ8 C8 O2 DOUB N N 13 EJ8 C8 N9 SING N N 14 EJ8 C4 N9 SING N N 15 EJ8 N9 "C1'" SING N N 16 EJ8 "C1'" "C2'" SING N N 17 EJ8 "C1'" "O4'" SING N N 18 EJ8 "C2'" "C3'" SING N N 19 EJ8 C9 CAA DOUB Y N 20 EJ8 C9 C10 SING Y N 21 EJ8 "O4'" "C4'" SING N N 22 EJ8 CAA C2 SING Y N 23 EJ8 "O3'" "C3'" SING N N 24 EJ8 "O3'" CAB SING N N 25 EJ8 "C3'" "C4'" SING N N 26 EJ8 C10 C11 DOUB Y N 27 EJ8 "C4'" "C5'" SING N N 28 EJ8 C2 CAB SING N N 29 EJ8 C2 C12 DOUB Y N 30 EJ8 C11 C12 SING Y N 31 EJ8 CAB O7 SING N N 32 EJ8 CAB P SING N N 33 EJ8 O7 "C5'" SING N N 34 EJ8 OP2 P DOUB N N 35 EJ8 P OP1 SING N N 36 EJ8 P OP3 SING N N 37 EJ8 "C2'" H1 SING N N 38 EJ8 "C2'" H2 SING N N 39 EJ8 "C1'" H3 SING N N 40 EJ8 O9 H4 SING N N 41 EJ8 O11 H5 SING N N 42 EJ8 C18 H6 SING N N 43 EJ8 C18 H7 SING N N 44 EJ8 C17 H8 SING N N 45 EJ8 C17 H9 SING N N 46 EJ8 C4 H10 SING N N 47 EJ8 N1 H11 SING N N 48 EJ8 "C3'" H12 SING N N 49 EJ8 "C4'" H13 SING N N 50 EJ8 "C5'" H14 SING N N 51 EJ8 "C5'" H15 SING N N 52 EJ8 OP1 H16 SING N N 53 EJ8 OP3 H17 SING N N 54 EJ8 CAA H18 SING N N 55 EJ8 C9 H19 SING N N 56 EJ8 C10 H20 SING N N 57 EJ8 C11 H21 SING N N 58 EJ8 C12 H22 SING N N 59 # 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 EJ8 InChI InChI 1.03 "InChI=1S/C18H22N2O11P2S/c21-16-11(9-34-10-32(23,24)25)7-20(17(22)19-16)15-6-13-14(30-15)8-29-18(31-13,33(26,27)28)12-4-2-1-3-5-12/h1-5,7,13-15H,6,8-10H2,(H,19,21,22)(H2,23,24,25)(H2,26,27,28)/t13-,14-,15-,18-/m1/s1" EJ8 InChIKey InChI 1.03 KFRRWRABRKBEOD-ATNYBXOESA-N EJ8 SMILES_CANONICAL CACTVS 3.385 "O[P](O)(=O)CSCC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" EJ8 SMILES CACTVS 3.385 "O[P](O)(=O)CSCC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" EJ8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)[C@]2(OC[C@@H]3[C@H](O2)C[C@@H](O3)N4C=C(C(=O)NC4=O)CSCP(=O)(O)O)P(=O)(O)O" EJ8 SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)CSCP(=O)(O)O)P(=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 EJ8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EJ8 "Create component" 2018-03-23 EBI EJ8 "Initial release" 2018-07-11 RCSB #