data_D5D # _chem_comp.id D5D _chem_comp.name "[(1S)-1-[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethyl] dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-12-15 _chem_comp.pdbx_modified_date 2025-11-07 _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 340.224 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D5D _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 8HMK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 D5D O2 O1 O 0 1 N N N N N N 225.680 251.695 210.667 -1.002 -1.231 0.319 O2 D5D 1 D5D O4 O2 O 0 1 N N N N N N 224.079 253.979 207.348 -5.344 -2.060 0.266 O4 D5D 2 D5D "C1'" C1 C 0 1 N N R N N N 225.322 253.714 212.523 -1.191 1.350 -0.336 "C1'" D5D 3 D5D C2 C2 C 0 1 N N N N N N 225.078 252.685 210.323 -2.139 -0.813 0.221 C2 D5D 4 D5D "C2'" C3 C 0 1 N N R N N N 226.445 254.643 212.955 -0.272 1.473 0.906 "C2'" D5D 5 D5D "C3'" C4 C 0 1 N N S N N N 226.118 254.828 214.427 1.093 1.824 0.266 "C3'" D5D 6 D5D C34 C5 C 0 1 N N N N N N 222.574 255.874 214.092 1.837 -0.240 -2.913 C34 D5D 7 D5D C4 C6 C 0 1 N N N N N N 224.483 253.866 208.482 -4.420 -1.308 0.044 C4 D5D 8 D5D "C4'" C7 C 0 1 N N S N N N 224.597 254.880 214.414 0.960 1.346 -1.192 "C4'" D5D 9 D5D C5 C8 C 0 1 N N N N N N 225.073 255.046 209.183 -4.674 0.030 -0.604 C5 D5D 10 D5D "C5'" C9 C 0 1 N N S N N N 224.017 256.267 214.370 2.052 0.320 -1.505 "C5'" D5D 11 D5D C6 C10 C 0 1 N N N N N N 224.632 255.063 210.630 -3.688 1.056 -0.048 C6 D5D 12 D5D N1 N1 N 0 1 N N N N N N 225.015 253.755 211.089 -2.339 0.488 -0.045 N1 D5D 13 D5D N3 N2 N 0 1 N N N N N N 224.453 252.739 209.163 -3.166 -1.666 0.377 N3 D5D 14 D5D "O2'" O3 O 0 1 N N N N N N 227.713 254.090 212.703 -0.717 2.522 1.768 "O2'" D5D 15 D5D "O3'" O4 O 0 1 N N N N N N 226.543 253.683 215.161 1.319 3.234 0.312 "O3'" D5D 16 D5D "O4'" O5 O 0 1 N N N N N N 224.183 254.150 213.231 -0.337 0.742 -1.328 "O4'" D5D 17 D5D "O5'" O6 O 0 1 N N N N N N 224.267 256.894 213.126 1.990 -0.745 -0.555 "O5'" D5D 18 D5D OP1 O7 O 0 1 N N N N N N 223.585 259.263 213.418 4.429 -1.375 -0.391 OP1 D5D 19 D5D OP2 O8 O 0 1 N N N N N N 226.007 258.527 213.843 3.492 0.096 1.433 OP2 D5D 20 D5D P P1 P 0 1 N N N N N N 224.748 258.400 213.052 3.216 -1.123 0.418 P D5D 21 D5D "H1'" H1 H 0 1 N N N N N N 225.582 252.685 212.814 -1.523 2.334 -0.666 "H1'" D5D 22 D5D "H2'" H2 H 0 1 N N N N N N 226.332 255.607 212.438 -0.217 0.526 1.445 "H2'" D5D 23 D5D "H3'" H3 H 0 1 N N N N N N 226.545 255.764 214.816 1.900 1.293 0.772 "H3'" D5D 24 D5D H4 H4 H 0 1 N N N N N N 222.161 255.349 214.966 1.883 0.573 -3.638 H4 D5D 25 D5D H5 H5 H 0 1 N N N N N N 221.980 256.778 213.893 2.614 -0.970 -3.136 H5 D5D 26 D5D H6 H6 H 0 1 N N N N N N 222.537 255.211 213.215 0.860 -0.720 -2.968 H6 D5D 27 D5D "H4'" H7 H 0 1 N N N N N N 224.222 254.367 215.312 1.046 2.196 -1.870 "H4'" D5D 28 D5D H51 H8 H 0 1 N N N N N N 226.170 254.985 209.137 -4.537 -0.055 -1.682 H51 D5D 29 D5D H52 H9 H 0 1 N N N N N N 224.736 255.969 208.689 -5.694 0.350 -0.391 H52 D5D 30 D5D "H5'" H10 H 0 1 N N N N N N 224.170 256.872 215.276 3.028 0.801 -1.451 "H5'" D5D 31 D5D H61 H11 H 0 1 N N N N N N 225.153 255.850 211.195 -3.705 1.951 -0.671 H61 D5D 32 D5D H62 H12 H 0 1 N N N N N N 223.545 255.210 210.712 -3.972 1.318 0.971 H62 D5D 33 D5D HN3 H13 H 0 1 N N N N N N 223.966 251.941 208.808 -3.001 -2.552 0.734 HN3 D5D 34 D5D "HO2'" H14 H 0 0 N N N N N N 228.386 254.698 212.986 -0.174 2.638 2.560 "HO2'" D5D 35 D5D "HO3'" H15 H 0 0 N Y N N N N 226.337 253.802 216.081 1.352 3.598 1.208 "HO3'" D5D 36 D5D HOP2 H16 H 0 0 N N N N N N 225.892 259.184 214.519 2.738 0.317 1.997 HOP2 D5D 37 D5D OP3 OP3 O 0 1 N Y N N N N 225.033 258.641 211.494 2.846 -2.446 1.258 OP3 D5D 38 D5D HOP3 H17 H 0 0 N N N N N N 224.409 259.270 211.151 3.541 -2.733 1.866 HOP3 D5D 39 # 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 D5D O4 C4 DOUB N N 1 D5D C4 N3 SING N N 2 D5D C4 C5 SING N N 3 D5D N3 C2 SING N N 4 D5D C5 C6 SING N N 5 D5D C2 O2 DOUB N N 6 D5D C2 N1 SING N N 7 D5D C6 N1 SING N N 8 D5D N1 "C1'" SING N N 9 D5D "C1'" "C2'" SING N N 10 D5D "C1'" "O4'" SING N N 11 D5D "O2'" "C2'" SING N N 12 D5D "C2'" "C3'" SING N N 13 D5D P "O5'" SING N N 14 D5D P OP1 DOUB N N 15 D5D P OP2 SING N N 16 D5D "O5'" "C5'" SING N N 17 D5D "O4'" "C4'" SING N N 18 D5D C34 "C5'" SING N N 19 D5D "C5'" "C4'" SING N N 20 D5D "C4'" "C3'" SING N N 21 D5D "C3'" "O3'" SING N N 22 D5D "C1'" "H1'" SING N N 23 D5D "C2'" "H2'" SING N N 24 D5D "C3'" "H3'" SING N N 25 D5D C34 H4 SING N N 26 D5D C34 H5 SING N N 27 D5D C34 H6 SING N N 28 D5D "C4'" "H4'" SING N N 29 D5D C5 H51 SING N N 30 D5D C5 H52 SING N N 31 D5D "C5'" "H5'" SING N N 32 D5D C6 H61 SING N N 33 D5D C6 H62 SING N N 34 D5D N3 HN3 SING N N 35 D5D "O2'" "HO2'" SING N N 36 D5D "O3'" "HO3'" SING N N 37 D5D OP2 HOP2 SING N N 38 D5D P OP3 SING N N 39 D5D OP3 HOP3 SING N N 40 # 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 D5D InChI InChI 1.06 "InChI=1S/C10H17N2O9P/c1-4(21-22(17,18)19)8-6(14)7(15)9(20-8)12-3-2-5(13)11-10(12)16/h4,6-9,14-15H,2-3H2,1H3,(H,11,13,16)(H2,17,18,19)/t4-,6-,7+,8+,9+/m0/s1" D5D InChIKey InChI 1.06 UTNZYCCMZBSWKD-IHMGDUAMSA-N D5D SMILES_CANONICAL CACTVS 3.385 "C[C@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CCC(=O)NC2=O" D5D SMILES CACTVS 3.385 "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](O)[CH]1O)N2CCC(=O)NC2=O" D5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2CCC(=O)NC2=O)O)O)OP(=O)(O)O" D5D SMILES "OpenEye OEToolkits" 2.0.7 "CC(C1C(C(C(O1)N2CCC(=O)NC2=O)O)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id D5D _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(1~{S})-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethyl] 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 D5D "Create component" 2022-12-15 PDBJ D5D "Initial release" 2025-11-12 RCSB #