data_B8H # _chem_comp.id B8H _chem_comp.name "[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-25 _chem_comp.pdbx_modified_date 2019-05-06 _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 338.208 _chem_comp.one_letter_code U _chem_comp.three_letter_code B8H _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 B8H N1 N1 N 0 1 N N N 260.734 293.041 219.842 -4.314 -0.877 -0.749 N1 B8H 1 B8H C2 C1 C 0 1 N N N 260.266 294.152 220.561 -4.280 -1.467 0.460 C2 B8H 2 B8H C4 C2 C 0 1 N N N 260.861 295.594 218.858 -2.209 -0.491 0.925 C4 B8H 3 B8H "C1'" C3 C 0 1 N N S 261.934 294.687 216.721 -1.088 1.013 -0.783 "C1'" B8H 4 B8H "C2'" C4 C 0 1 N N R 263.409 295.076 216.824 -1.013 2.260 0.118 "C2'" B8H 5 B8H "C3'" C5 C 0 1 N N S 264.073 293.721 216.654 0.408 2.202 0.729 "C3'" B8H 6 B8H "C4'" C6 C 0 1 N N R 263.206 293.077 215.594 1.154 1.283 -0.271 "C4'" B8H 7 B8H C5 C7 C 0 1 N N N 261.352 294.457 218.069 -2.230 0.132 -0.346 C5 B8H 8 B8H "C5'" C8 C 0 1 N N N 263.259 291.577 215.522 2.346 0.604 0.407 "C5'" B8H 9 B8H C6 C9 C 0 1 N N N 261.239 293.199 218.634 -3.286 -0.074 -1.161 C6 B8H 10 B8H CN1 C10 C 0 1 N N N 260.660 291.685 220.383 -5.460 -1.102 -1.634 CN1 B8H 11 B8H N3 N2 N 0 1 N N N 260.340 295.380 220.061 -3.240 -1.279 1.293 N3 B8H 12 B8H O2 O1 O 0 1 N N N 259.781 294.000 221.696 -5.203 -2.180 0.805 O2 B8H 13 B8H "O2'" O2 O 0 1 N N N 263.725 295.919 215.730 -1.179 3.448 -0.657 "O2'" B8H 14 B8H "O3'" O3 O 0 1 N N N 265.446 293.767 216.323 1.000 3.502 0.768 "O3'" B8H 15 B8H O4 O4 O 0 1 N N N 260.931 296.746 218.391 -1.268 -0.320 1.678 O4 B8H 16 B8H "O4'" O5 O 0 1 N N N 261.867 293.509 215.944 0.156 0.307 -0.640 "O4'" B8H 17 B8H "O5'" O6 O 0 1 N N N 262.699 290.975 216.675 3.022 -0.227 -0.538 "O5'" B8H 18 B8H OP1 O7 O 0 1 N N N 261.822 289.002 217.966 4.897 -1.801 -1.498 OP1 B8H 19 B8H OP2 O8 O 0 1 N N N 262.931 288.743 215.634 5.365 -0.206 0.402 OP2 B8H 20 B8H P P1 P 0 1 N N N 262.061 289.525 216.579 4.327 -1.095 -0.168 P B8H 21 B8H O1 O9 O 0 1 N Y N 260.657 289.767 215.844 3.933 -2.222 0.912 O1 B8H 22 B8H H1 H1 H 0 1 N N N 261.388 295.503 216.225 -1.229 1.314 -1.821 H1 B8H 23 B8H H2 H2 H 0 1 N N N 263.642 295.524 217.801 -1.768 2.209 0.903 H2 B8H 24 B8H H3 H3 H 0 1 N N N 263.942 293.158 217.590 0.386 1.757 1.724 H3 B8H 25 B8H H4 H4 H 0 1 N N N 263.482 293.490 214.613 1.479 1.849 -1.143 H4 B8H 26 B8H H5 H5 H 0 1 N N N 262.697 291.243 214.637 3.033 1.363 0.780 H5 B8H 27 B8H H6 H6 H 0 1 N N N 264.309 291.262 215.430 1.992 -0.006 1.239 H6 B8H 28 B8H H7 H7 H 0 1 N N N 261.569 292.334 218.078 -3.319 0.392 -2.135 H7 B8H 29 B8H H8 H8 H 0 1 N N N 260.220 291.715 221.391 -6.173 -1.765 -1.144 H8 B8H 30 B8H H9 H9 H 0 1 N N N 260.033 291.063 219.728 -5.942 -0.149 -1.852 H9 B8H 31 B8H H10 H10 H 0 1 N N N 261.672 291.257 220.438 -5.118 -1.557 -2.563 H10 B8H 32 B8H H11 H11 H 0 1 N N N 259.999 296.153 220.597 -3.233 -1.709 2.162 H11 B8H 33 B8H H12 H12 H 0 1 N N N 263.304 296.763 215.848 -1.140 4.265 -0.140 H12 B8H 34 B8H H13 H13 H 0 1 N N N 265.929 294.181 217.029 0.516 4.139 1.311 H13 B8H 35 B8H H14 H14 H 0 1 N N N 262.286 288.181 218.080 5.685 -2.342 -1.349 H14 B8H 36 B8H H15 H15 H 0 1 N N N 260.678 289.369 214.982 3.256 -2.841 0.605 H15 B8H 37 # # 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 B8H "C5'" "C4'" SING N N 1 B8H "C5'" "O5'" SING N N 2 B8H "C4'" "O4'" SING N N 3 B8H "C4'" "C3'" SING N N 4 B8H OP2 P DOUB N N 5 B8H "O2'" "C2'" SING N N 6 B8H "O4'" "C1'" SING N N 7 B8H "O3'" "C3'" SING N N 8 B8H P "O5'" SING N N 9 B8H P OP1 SING N N 10 B8H "C3'" "C2'" SING N N 11 B8H "C1'" "C2'" SING N N 12 B8H "C1'" C5 SING N N 13 B8H C5 C6 DOUB N N 14 B8H C5 C4 SING N N 15 B8H O4 C4 DOUB N N 16 B8H C6 N1 SING N N 17 B8H C4 N3 SING N N 18 B8H N1 CN1 SING N N 19 B8H N1 C2 SING N N 20 B8H N3 C2 SING N N 21 B8H C2 O2 DOUB N N 22 B8H P O1 SING N N 23 B8H "C1'" H1 SING N N 24 B8H "C2'" H2 SING N N 25 B8H "C3'" H3 SING N N 26 B8H "C4'" H4 SING N N 27 B8H "C5'" H5 SING N N 28 B8H "C5'" H6 SING N N 29 B8H C6 H7 SING N N 30 B8H CN1 H8 SING N N 31 B8H CN1 H9 SING N N 32 B8H CN1 H10 SING N N 33 B8H N3 H11 SING N N 34 B8H "O2'" H12 SING N N 35 B8H "O3'" H13 SING N N 36 B8H OP1 H14 SING N N 37 B8H O1 H15 SING N N 38 # # 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 B8H InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-12-2-4(9(15)11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1" B8H InChIKey InChI 1.03 VORAOZTXNOXTGQ-XUTVFYLZSA-N B8H SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O" B8H SMILES CACTVS 3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O" B8H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" B8H SMILES "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id B8H _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~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-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 B8H "Create component" 2017-09-25 EBI B8H "Other modification" 2017-11-02 EBI B8H "Initial release" 2018-01-24 RCSB B8H "Modify one letter code" 2019-05-06 EBI ##