data_M5Q # _chem_comp.id M5Q _chem_comp.name "[(1S)-1-[(2S,3R,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]ethyl] dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H18 N3 O8 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 351.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code M5Q _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 M5Q "C1'" C1 C 0 1 N N R N N N 231.600 261.679 220.869 -1.143 1.131 -0.760 "C1'" M5Q 1 M5Q C2 C2 C 0 1 N N N N N N 232.019 259.503 221.882 -2.062 -0.983 0.017 C2 M5Q 2 M5Q "C2'" C3 C 0 1 N N R N N N 232.582 261.601 219.704 -0.338 1.439 0.528 "C2'" M5Q 3 M5Q "C3'" C4 C 0 1 N N R N N N 231.653 261.792 218.524 1.063 1.777 -0.038 "C3'" M5Q 4 M5Q C34 C5 C 0 1 N N N N N N 228.723 264.197 218.836 2.146 -0.606 -2.878 C34 M5Q 5 M5Q C4 C6 C 0 1 N N N N N N 230.398 258.051 222.157 -4.330 -1.412 0.106 C4 M5Q 6 M5Q "C4'" C7 C 0 1 N N S N N N 230.684 262.814 219.056 1.072 1.128 -1.436 "C4'" M5Q 7 M5Q C5 C8 C 0 1 N N N N N N 229.431 258.913 221.599 -4.592 -0.118 -0.388 C5 M5Q 8 M5Q "C5'" C9 C 0 1 N N S N N N 229.374 262.915 218.334 2.220 0.122 -1.534 "C5'" M5Q 9 M5Q C6 C10 C 0 1 N N N N N N 229.851 260.102 221.183 -3.550 0.700 -0.668 C6 M5Q 10 M5Q N1 N1 N 0 1 N N N N N N 231.163 260.351 221.339 -2.279 0.256 -0.461 N1 M5Q 11 M5Q N3 N2 N 0 1 N N N N N N 231.672 258.295 222.320 -3.076 -1.802 0.292 N3 M5Q 12 M5Q N4 N3 N 0 1 N N N N N N 229.959 256.867 222.557 -5.370 -2.266 0.394 N4 M5Q 13 M5Q O2 O1 O 0 1 N N N N N N 233.199 259.801 222.006 -0.917 -1.365 0.197 O2 M5Q 14 M5Q "O2'" O2 O 0 1 N N N N N N 233.456 262.703 219.803 -0.892 2.560 1.220 "O2'" M5Q 15 M5Q "O3'" O3 O 0 1 N N N N N N 232.303 262.207 217.341 1.235 3.192 -0.142 "O3'" M5Q 16 M5Q "O4'" O4 O 0 1 N N N N N N 230.465 262.377 220.412 -0.188 0.454 -1.604 "O4'" M5Q 17 M5Q "O5'" O5 O 0 1 N N N N N N 228.527 261.835 218.657 2.115 -0.827 -0.471 "O5'" M5Q 18 M5Q OP1 O6 O 0 1 N N N N N N 226.612 261.569 217.129 4.551 -1.326 -0.037 OP1 M5Q 19 M5Q OP2 O7 O 0 1 N N N N N N 228.823 260.595 216.547 3.411 0.305 1.517 OP2 M5Q 20 M5Q P P1 P 0 1 N N N N N N 227.841 260.948 217.538 3.265 -1.035 0.636 P M5Q 21 M5Q CM2 C11 C 0 1 N N N N N N 234.766 262.350 220.089 -1.870 2.211 2.202 CM2 M5Q 22 M5Q "H1'" H1 H 0 1 N N N N N N 232.077 262.223 221.698 -1.484 2.054 -1.230 "H1'" M5Q 23 M5Q "H2'" H2 H 0 1 N N N N N N 233.098 260.630 219.669 -0.295 0.566 1.178 "H2'" M5Q 24 M5Q "H3'" H3 H 0 1 N N N N N N 231.112 260.851 218.346 1.841 1.343 0.590 "H3'" M5Q 25 M5Q H34 H4 H 0 1 N N N N N N 229.368 265.055 218.595 2.227 0.118 -3.688 H34 M5Q 26 M5Q H35 H5 H 0 1 N N N N N N 227.744 264.326 218.350 2.964 -1.323 -2.948 H35 M5Q 27 M5Q H36 H6 H 0 1 N N N N N N 228.586 264.136 219.926 1.195 -1.132 -2.954 H36 M5Q 28 M5Q "H4'" H7 H 0 1 N N N N N N 231.170 263.801 219.056 1.183 1.897 -2.200 "H4'" M5Q 29 M5Q H5 H8 H 0 1 N N N N N N 228.395 258.619 221.514 -5.608 0.214 -0.545 H5 M5Q 30 M5Q "H5'" H9 H 0 1 N N N N N N 229.544 262.983 217.249 3.172 0.648 -1.458 "H5'" M5Q 31 M5Q H6 H10 H 0 1 N N N N N N 229.179 260.826 220.746 -3.725 1.695 -1.052 H6 M5Q 32 M5Q HN41 H11 H 0 0 N N N N N N 230.594 256.209 222.962 -5.186 -3.156 0.734 HN41 M5Q 33 M5Q HN42 H12 H 0 0 N N N N N N 228.993 256.631 222.454 -6.286 -1.979 0.257 HN42 M5Q 34 M5Q "HO3'" H13 H 0 0 N N N N N N 232.900 261.527 217.052 1.237 3.652 0.708 "HO3'" M5Q 35 M5Q HOP2 H15 H 0 0 N N N N N N 228.505 260.838 215.685 2.604 0.556 1.987 HOP2 M5Q 36 M5Q H16 H16 H 0 1 N N N N N N 235.386 263.257 220.151 -2.243 3.116 2.682 H16 M5Q 37 M5Q H17 H17 H 0 1 N N N N N N 234.800 261.817 221.050 -2.697 1.689 1.721 H17 M5Q 38 M5Q H18 H18 H 0 1 N N N N N N 235.152 261.696 219.293 -1.418 1.562 2.951 H18 M5Q 39 M5Q OP3 O8 O 0 1 N N N N N N 227.467 259.613 218.322 2.870 -2.267 1.594 OP3 M5Q 40 M5Q HOP3 H14 H 0 0 N N N N N N 226.522 259.516 218.350 3.520 -2.450 2.287 HOP3 M5Q 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 M5Q OP2 P SING N N 1 M5Q OP1 P DOUB N N 2 M5Q "O3'" "C3'" SING N N 3 M5Q P "O5'" SING N N 4 M5Q "C5'" "O5'" SING N N 5 M5Q "C5'" C34 SING N N 6 M5Q "C5'" "C4'" SING N N 7 M5Q "C3'" "C4'" SING N N 8 M5Q "C3'" "C2'" SING N N 9 M5Q "C4'" "O4'" SING N N 10 M5Q "C2'" "O2'" SING N N 11 M5Q "C2'" "C1'" SING N N 12 M5Q "O2'" CM2 SING N N 13 M5Q "O4'" "C1'" SING N N 14 M5Q "C1'" N1 SING N N 15 M5Q C6 N1 SING N N 16 M5Q C6 C5 DOUB N N 17 M5Q N1 C2 SING N N 18 M5Q C5 C4 SING N N 19 M5Q C2 O2 DOUB N N 20 M5Q C2 N3 SING N N 21 M5Q C4 N3 DOUB N N 22 M5Q C4 N4 SING N N 23 M5Q "C1'" "H1'" SING N N 24 M5Q "C2'" "H2'" SING N N 25 M5Q "C3'" "H3'" SING N N 26 M5Q C34 H34 SING N N 27 M5Q C34 H35 SING N N 28 M5Q C34 H36 SING N N 29 M5Q "C4'" "H4'" SING N N 30 M5Q C5 H5 SING N N 31 M5Q "C5'" "H5'" SING N N 32 M5Q C6 H6 SING N N 33 M5Q N4 HN41 SING N N 34 M5Q N4 HN42 SING N N 35 M5Q "O3'" "HO3'" SING N N 36 M5Q OP2 HOP2 SING N N 37 M5Q CM2 H16 SING N N 38 M5Q CM2 H17 SING N N 39 M5Q CM2 H18 SING N N 40 M5Q P OP3 SING N N 41 M5Q OP3 HOP3 SING N N 42 # 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 M5Q InChI InChI 1.06 "InChI=1S/C11H18N3O8P/c1-5(22-23(17,18)19)8-7(15)9(20-2)10(21-8)14-4-3-6(12)13-11(14)16/h3-5,7-10,15H,1-2H3,(H2,12,13,16)(H2,17,18,19)/t5-,7+,8+,9+,10+/m0/s1" M5Q InChIKey InChI 1.06 OBLDPPWBFVCFRR-BOHATCBPSA-N M5Q SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=CC(=NC2=O)N)[C@H](C)O[P](O)(O)=O" M5Q SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](O[CH]1N2C=CC(=NC2=O)N)[CH](C)O[P](O)(O)=O" M5Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)OC)O)OP(=O)(O)O" M5Q SMILES "OpenEye OEToolkits" 2.0.7 "CC(C1C(C(C(O1)N2C=CC(=NC2=O)N)OC)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id M5Q _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~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-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 M5Q "Create component" 2022-12-15 PDBJ M5Q "Initial release" 2025-11-12 RCSB #