data_8EF # _chem_comp.id 8EF _chem_comp.name "2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H20 N4 O7 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-06-20 _chem_comp.pdbx_modified_date 2018-04-20 _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 426.322 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 5XRV _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 8EF "C4'" C1 C 0 1 Y N N -12.878 -32.823 -26.011 4.874 -1.090 -0.839 "C4'" 8EF 1 8EF "C5'" C2 C 0 1 Y N N -12.984 -32.981 -27.411 4.720 -0.606 0.462 "C5'" 8EF 2 8EF "C6'" C3 C 0 1 Y N N -11.801 -33.067 -28.113 4.297 -1.482 1.442 "C6'" 8EF 3 8EF "N1'" N1 N 0 1 Y N N -10.584 -33.007 -27.431 4.052 -2.744 1.119 "N1'" 8EF 4 8EF "N3'" N2 N 0 1 Y N N -11.685 -32.765 -25.381 4.608 -2.370 -1.084 "N3'" 8EF 5 8EF O2B O1 O 0 1 N N N -20.131 -40.433 -25.582 -6.261 -1.470 -1.258 O2B 8EF 6 8EF PB P1 P 0 1 N N N -18.969 -41.327 -26.155 -5.787 -0.992 0.205 PB 8EF 7 8EF O1B O2 O 0 1 N N N -19.184 -41.248 -27.769 -6.543 0.218 0.597 O1B 8EF 8 8EF O3B O3 O 0 1 N N N -18.926 -42.762 -25.800 -6.064 -2.167 1.270 O3B 8EF 9 8EF O3A O4 O 0 1 N N N -17.615 -40.449 -26.028 -4.213 -0.655 0.175 O3A 8EF 10 8EF PA P2 P 0 1 N N N -16.099 -40.953 -26.266 -3.350 0.612 -0.318 PA 8EF 11 8EF O2A O5 O 0 1 N N N -15.015 -40.016 -25.574 -3.292 0.629 -1.927 O2A 8EF 12 8EF O1A O6 O 0 1 N N N -15.872 -42.140 -27.118 -3.983 1.859 0.166 O1A 8EF 13 8EF O7 O7 O 0 1 N N N -15.989 -39.973 -27.563 -1.856 0.505 0.271 O7 8EF 14 8EF C7 C4 C 0 1 N N N -15.440 -38.696 -27.317 -0.876 1.531 0.099 C7 8EF 15 8EF C6 C5 C 0 1 N N N -15.969 -37.726 -28.344 0.428 1.110 0.781 C6 8EF 16 8EF C5 C6 C 0 1 N N S -15.551 -36.426 -27.659 1.477 2.209 0.596 C5 8EF 17 8EF C4 C7 C 0 1 N N N -14.897 -35.405 -28.401 2.778 1.823 1.271 C4 8EF 18 8EF CM4 C8 C 0 1 N N N -14.116 -35.620 -29.463 2.872 1.656 2.577 CM4 8EF 19 8EF S1 S1 S 0 1 N N N -16.812 -35.536 -26.694 1.946 2.365 -1.171 S1 8EF 20 8EF C2 C9 C 0 1 N N N -16.129 -34.012 -27.147 3.755 2.374 -0.855 C2 8EF 21 8EF N3 N3 N 0 1 N N N -14.836 -34.274 -27.689 3.852 1.660 0.432 N3 8EF 22 8EF "C7'" C10 C 0 1 N N N -14.178 -33.071 -28.180 5.010 0.837 0.788 "C7'" 8EF 23 8EF "C2'" C11 C 0 1 Y N N -10.551 -32.845 -26.092 4.207 -3.171 -0.118 "C2'" 8EF 24 8EF CM2 C12 C 0 1 N N N -9.329 -32.761 -25.415 3.916 -4.615 -0.437 CM2 8EF 25 8EF "N4'" N4 N 0 1 N N N -13.983 -32.738 -25.280 5.290 -0.249 -1.858 "N4'" 8EF 26 8EF H1 H1 H 0 1 N N N -11.815 -33.180 -29.187 4.168 -1.143 2.459 H1 8EF 27 8EF H2 H2 H 0 1 N N N -20.647 -40.085 -26.300 -5.806 -2.260 -1.580 H2 8EF 28 8EF H3 H3 H 0 1 N N N -19.032 -43.286 -26.585 -6.994 -2.422 1.341 H3 8EF 29 8EF H4 H4 H 0 1 N N N -14.144 -40.329 -25.786 -2.888 -0.160 -2.314 H4 8EF 30 8EF H5 H5 H 0 1 N N N -14.343 -38.746 -27.388 -0.696 1.687 -0.964 H5 8EF 31 8EF H6 H6 H 0 1 N N N -15.727 -38.359 -26.310 -1.237 2.457 0.546 H6 8EF 32 8EF H7 H7 H 0 1 N N N -17.060 -37.801 -28.462 0.248 0.955 1.844 H7 8EF 33 8EF H8 H8 H 0 1 N N N -15.485 -37.853 -29.323 0.789 0.184 0.334 H8 8EF 34 8EF H9 H9 H 0 1 N N N -14.837 -36.737 -26.882 1.108 3.159 0.982 H9 8EF 35 8EF H10 H10 H 0 1 N N N -13.945 -36.627 -29.813 3.818 1.381 3.019 H10 8EF 36 8EF H11 H11 H 0 1 N N N -13.655 -34.786 -29.972 2.002 1.794 3.203 H11 8EF 37 8EF H12 H12 H 0 1 N N N -16.043 -33.360 -26.265 4.288 1.836 -1.638 H12 8EF 38 8EF H13 H13 H 0 1 N N N -16.763 -33.525 -27.903 4.128 3.394 -0.765 H13 8EF 39 8EF H14 H14 H 0 1 N N N -13.945 -33.164 -29.251 5.211 0.935 1.855 H14 8EF 40 8EF H15 H15 H 0 1 N N N -14.812 -32.187 -28.019 5.880 1.170 0.223 H15 8EF 41 8EF H16 H16 H 0 1 N N N -8.503 -32.847 -26.136 2.868 -4.720 -0.719 H16 8EF 42 8EF H17 H17 H 0 1 N N N -9.263 -31.793 -24.896 4.549 -4.939 -1.263 H17 8EF 43 8EF H18 H18 H 0 1 N N N -9.260 -33.577 -24.680 4.120 -5.228 0.440 H18 8EF 44 8EF H19 H19 H 0 1 N N N -13.738 -32.638 -24.316 5.250 -0.548 -2.780 H19 8EF 45 8EF H20 H20 H 0 1 N N N -14.516 -31.944 -25.573 5.622 0.638 -1.650 H20 8EF 46 # 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 8EF CM4 C4 DOUB N N 1 8EF C4 N3 SING N N 2 8EF C4 C5 SING N N 3 8EF C6 C5 SING N N 4 8EF C6 C7 SING N N 5 8EF "C7'" N3 SING N N 6 8EF "C7'" "C5'" SING N N 7 8EF "C6'" "N1'" DOUB Y N 8 8EF "C6'" "C5'" SING Y N 9 8EF O1B PB DOUB N N 10 8EF N3 C2 SING N N 11 8EF C5 S1 SING N N 12 8EF O7 C7 SING N N 13 8EF O7 PA SING N N 14 8EF "N1'" "C2'" SING Y N 15 8EF "C5'" "C4'" DOUB Y N 16 8EF C2 S1 SING N N 17 8EF O1A PA DOUB N N 18 8EF PA O3A SING N N 19 8EF PA O2A SING N N 20 8EF PB O3A SING N N 21 8EF PB O3B SING N N 22 8EF PB O2B SING N N 23 8EF "C2'" CM2 SING N N 24 8EF "C2'" "N3'" DOUB Y N 25 8EF "C4'" "N3'" SING Y N 26 8EF "C4'" "N4'" SING N N 27 8EF "C6'" H1 SING N N 28 8EF O2B H2 SING N N 29 8EF O3B H3 SING N N 30 8EF O2A H4 SING N N 31 8EF C7 H5 SING N N 32 8EF C7 H6 SING N N 33 8EF C6 H7 SING N N 34 8EF C6 H8 SING N N 35 8EF C5 H9 SING N N 36 8EF CM4 H10 SING N N 37 8EF CM4 H11 SING N N 38 8EF C2 H12 SING N N 39 8EF C2 H13 SING N N 40 8EF "C7'" H14 SING N N 41 8EF "C7'" H15 SING N N 42 8EF CM2 H16 SING N N 43 8EF CM2 H17 SING N N 44 8EF CM2 H18 SING N N 45 8EF "N4'" H19 SING N N 46 8EF "N4'" H20 SING N N 47 # 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 8EF InChI InChI 1.03 "InChI=1S/C12H20N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,11H,1,3-4,6-7H2,2H3,(H,20,21)(H2,13,14,15)(H2,17,18,19)/t11-/m0/s1" 8EF InChIKey InChI 1.03 YBJKPSYOFQHZDJ-NSHDSACASA-N 8EF SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CN2CS[C@@H](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)c(N)n1" 8EF SMILES CACTVS 3.385 "Cc1ncc(CN2CS[CH](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)c(N)n1" 8EF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2CS[C@H](C2=C)CCOP(=O)(O)OP(=O)(O)O" 8EF SMILES "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2CSC(C2=C)CCOP(=O)(O)OP(=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 8EF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[(5~{S})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen 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 8EF "Create component" 2017-06-20 PDBJ 8EF "Initial release" 2018-04-25 RCSB #