data_EAN # _chem_comp.id EAN _chem_comp.name "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-03-12 _chem_comp.pdbx_modified_date 2019-05-06 _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 360.256 _chem_comp.one_letter_code T _chem_comp.three_letter_code EAN _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 6GN4 _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 EAN C7 C1 C 0 1 N N N 1.891 -4.728 -9.765 3.154 -1.614 -2.517 C7 EAN 1 EAN C6 C2 C 0 1 N N N 4.262 -4.211 -10.396 2.003 -0.462 -0.645 C6 EAN 2 EAN C5 C3 C 0 1 N N N 2.978 -3.772 -10.225 3.145 -0.975 -1.152 C5 EAN 3 EAN C4 C4 C 0 1 N N N 2.628 -2.375 -10.484 4.332 -0.903 -0.385 C4 EAN 4 EAN C2 C5 C 0 1 N N N 5.021 -1.999 -11.074 3.149 0.185 1.311 C2 EAN 5 EAN P P1 P 0 1 N N N 6.734 -9.044 -10.671 -3.110 -1.582 0.389 P EAN 6 EAN O1P O1 O 0 1 N N N 7.919 -8.538 -11.407 -4.077 -0.855 1.241 O1P EAN 7 EAN O2P O2 O 0 1 N N N 6.903 -10.096 -9.644 -3.756 -2.978 -0.086 O2P EAN 8 EAN "O5'" O3 O 0 1 N N N 6.012 -7.778 -9.967 -2.755 -0.688 -0.902 "O5'" EAN 9 EAN "C5'" C6 C 0 1 N N R 6.807 -6.852 -9.264 -2.263 0.650 -0.811 "C5'" EAN 10 EAN "C4'" C7 C 0 1 N N S 7.547 -5.781 -10.050 -1.407 1.005 0.418 "C4'" EAN 11 EAN "O4'" O4 O 0 1 N N N 6.712 -5.278 -11.101 -0.359 0.027 0.558 "O4'" EAN 12 EAN "C1'" C8 C 0 1 N N R 6.679 -3.842 -11.063 0.776 0.685 1.139 "C1'" EAN 13 EAN N1 N1 N 0 1 N N N 5.275 -3.360 -10.827 2.013 0.119 0.593 N1 EAN 14 EAN O4 O5 O 0 1 N N N 1.500 -1.895 -10.379 5.374 -1.358 -0.822 O4 EAN 15 EAN N3 N2 N 0 1 N N N 3.702 -1.573 -10.886 4.299 -0.327 0.833 N3 EAN 16 EAN O2 O6 O 0 1 N N N 5.898 -1.215 -11.435 3.134 0.702 2.411 O2 EAN 17 EAN "C3'" C9 C 0 1 N N S 7.862 -4.637 -9.110 -0.653 2.306 0.004 "C3'" EAN 18 EAN "C2'" C10 C 0 1 N N N 7.610 -3.385 -9.942 0.679 2.178 0.775 "C2'" EAN 19 EAN "C7'" C11 C 0 1 N N N 6.878 -4.800 -7.922 -0.397 2.096 -1.505 "C7'" EAN 20 EAN "C6'" C12 C 0 1 N N S 6.346 -6.226 -7.976 -1.621 1.343 -2.024 "C6'" EAN 21 EAN "C8'" C13 C 0 1 N N N 7.392 -7.297 -7.951 -3.008 1.769 -1.543 "C8'" EAN 22 EAN "O3'" O7 O 0 1 N N N 9.220 -4.750 -8.685 -1.370 3.506 0.299 "O3'" EAN 23 EAN O3P O8 O 0 1 N Y N 5.653 -9.584 -11.756 -1.767 -1.871 1.228 O3P EAN 24 EAN H73 H1 H 0 1 N N N 2.321 -5.730 -9.618 3.376 -0.859 -3.271 H73 EAN 25 EAN H71 H2 H 0 1 N N N 1.464 -4.369 -8.817 3.916 -2.393 -2.548 H71 EAN 26 EAN H72 H3 H 0 1 N N N 1.100 -4.778 -10.528 2.178 -2.054 -2.719 H72 EAN 27 EAN H6 H4 H 0 1 N N N 4.496 -5.245 -10.191 1.087 -0.507 -1.216 H6 EAN 28 EAN H1 H5 H 0 1 N N N 7.821 -10.333 -9.581 -3.996 -3.569 0.641 H1 EAN 29 EAN "H4'" H6 H 0 1 N N N 8.481 -6.198 -10.455 -2.002 1.130 1.323 "H4'" EAN 30 EAN "H1'" H7 H 0 1 N N N 7.045 -3.432 -12.016 0.761 0.564 2.222 "H1'" EAN 31 EAN H3 H8 H 0 1 N N N 3.509 -0.606 -11.054 5.109 -0.271 1.364 H3 EAN 32 EAN "H2'" H9 H 0 1 N N N 8.553 -2.998 -10.355 0.656 2.789 1.677 "H2'" EAN 33 EAN "H2''" H10 H 0 0 N N N 7.129 -2.605 -9.333 1.516 2.469 0.139 "H2''" EAN 34 EAN "H7'" H11 H 0 1 N N N 7.403 -4.629 -6.971 -0.288 3.057 -2.008 "H7'" EAN 35 EAN "H7''" H12 H 0 0 N N N 6.049 -4.084 -8.018 0.493 1.486 -1.658 "H7''" EAN 36 EAN "H6'" H13 H 0 1 N N N 5.335 -6.438 -7.598 -1.526 0.826 -2.979 "H6'" EAN 37 EAN "H8'" H14 H 0 1 N N N 7.150 -8.293 -7.551 -3.862 1.485 -2.158 "H8'" EAN 38 EAN "H8''" H15 H 0 0 N N N 8.432 -7.043 -7.699 -3.092 2.732 -1.039 "H8''" EAN 39 EAN H2 H16 H 0 1 N N N 9.428 -4.036 -8.094 -0.905 4.315 0.044 H2 EAN 40 EAN H4 H17 H 0 1 N N N 5.998 -9.466 -12.633 -1.087 -2.345 0.730 H4 EAN 41 # # 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 EAN O2 C2 DOUB N N 1 EAN O1P P DOUB N N 2 EAN "O4'" "C1'" SING N N 3 EAN "O4'" "C4'" SING N N 4 EAN C2 N3 SING N N 5 EAN C2 N1 SING N N 6 EAN "C1'" N1 SING N N 7 EAN "C1'" "C2'" SING N N 8 EAN N3 C4 SING N N 9 EAN N1 C6 SING N N 10 EAN P "O5'" SING N N 11 EAN P O2P SING N N 12 EAN C4 O4 DOUB N N 13 EAN C4 C5 SING N N 14 EAN C6 C5 DOUB N N 15 EAN C5 C7 SING N N 16 EAN "C4'" "C5'" SING N N 17 EAN "C4'" "C3'" SING N N 18 EAN "O5'" "C5'" SING N N 19 EAN "C2'" "C3'" SING N N 20 EAN "C5'" "C6'" SING N N 21 EAN "C5'" "C8'" SING N N 22 EAN "C3'" "O3'" SING N N 23 EAN "C3'" "C7'" SING N N 24 EAN "C6'" "C8'" SING N N 25 EAN "C6'" "C7'" SING N N 26 EAN P O3P SING N N 27 EAN C7 H73 SING N N 28 EAN C7 H71 SING N N 29 EAN C7 H72 SING N N 30 EAN C6 H6 SING N N 31 EAN O2P H1 SING N N 32 EAN "C4'" "H4'" SING N N 33 EAN "C1'" "H1'" SING N N 34 EAN N3 H3 SING N N 35 EAN "C2'" "H2'" SING N N 36 EAN "C2'" "H2''" SING N N 37 EAN "C7'" "H7'" SING N N 38 EAN "C7'" "H7''" SING N N 39 EAN "C6'" "H6'" SING N N 40 EAN "C8'" "H8'" SING N N 41 EAN "C8'" "H8''" SING N N 42 EAN "O3'" H2 SING N N 43 EAN O3P H4 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 EAN InChI InChI 1.03 "InChI=1S/C13H17N2O8P/c1-6-5-15(11(17)14-9(6)16)8-4-12(18)2-7-3-13(7,10(12)22-8)23-24(19,20)21/h5,7-8,10,18H,2-4H2,1H3,(H,14,16,17)(H2,19,20,21)/t7-,8-,10+,12+,13-/m1/s1" EAN InChIKey InChI 1.03 GOQODLUGMVNILT-ZIDZYHNGSA-N EAN SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@@]3(O)C[C@@H]4C[C@]4(O[P](O)(O)=O)[C@H]3O2)C(=O)NC1=O" EAN SMILES CACTVS 3.385 "CC1=CN([CH]2C[C]3(O)C[CH]4C[C]4(O[P](O)(O)=O)[CH]3O2)C(=O)NC1=O" EAN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@]3(C[C@@H]4C[C@@]4([C@H]3O2)OP(=O)(O)O)O" EAN SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC3(CC4CC4(C3O2)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id EAN _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 "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] 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 EAN "Create component" 2018-03-12 EBI EAN "Other modification" 2018-04-19 EBI EAN "Other modification" 2018-04-27 EBI EAN "Other modification" 2018-05-30 EBI EAN "Initial release" 2018-06-06 RCSB EAN "Modify one letter code" 2019-05-06 EBI ##