data_M3X # _chem_comp.id M3X _chem_comp.name "(2~{S})-2-azanyl-6-[[4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-1-ium-2-yl]amino]hexanoic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H27 N5 O9 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ;lysidine 5'-monophosphate ; _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2022-12-22 _chem_comp.pdbx_modified_date 2024-03-01 _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 452.377 _chem_comp.one_letter_code C _chem_comp.three_letter_code M3X _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 M3X N1 N1 N 1 1 Y N N N N N ? ? ? -0.682 1.714 0.217 N1 M3X 1 M3X C2 C1 C 0 1 Y N N N N N ? ? ? 0.605 1.998 0.078 C2 M3X 2 M3X C4 C2 C 0 1 Y N N N N N ? ? ? 0.177 4.262 0.002 C4 M3X 3 M3X C5 C3 C 0 1 Y N N N N N ? ? ? -1.186 3.993 0.143 C5 M3X 4 M3X C6 C4 C 0 1 Y N N N N N ? ? ? -1.591 2.677 0.250 C6 M3X 5 M3X N N2 N 0 1 N N N N N N ? ? ? 7.752 -0.144 -1.766 N M3X 6 M3X C C5 C 0 1 N N N N N N ? ? ? 8.305 -2.029 -0.335 C M3X 7 M3X O O1 O 0 1 N N N N N N ? ? ? 8.575 -2.546 0.874 O M3X 8 M3X CB C6 C 0 1 N N N N N N ? ? ? 6.024 -1.057 -0.289 CB M3X 9 M3X CG C7 C 0 1 N N N N N N ? ? ? 5.233 0.253 -0.280 CG M3X 10 M3X CD C8 C 0 1 N N N N N N ? ? ? 3.742 -0.053 -0.120 CD M3X 11 M3X CE C9 C 0 1 N N N N N N ? ? ? 2.951 1.256 -0.111 CE M3X 12 M3X CZ C10 C 0 1 N N S N N N ? ? ? 7.515 -0.751 -0.449 CZ M3X 13 M3X OXT O2 O 0 1 N N N N N N ? ? ? 8.695 -2.589 -1.332 OXT M3X 14 M3X "C1'" C11 C 0 1 N N R N N N ? ? ? -1.105 0.317 0.329 "C1'" M3X 15 M3X "C2'" C12 C 0 1 N N R N N N ? ? ? -1.077 -0.137 1.806 "C2'" M3X 16 M3X "C3'" C13 C 0 1 N N S N N N ? ? ? -2.306 -1.064 1.937 "C3'" M3X 17 M3X "C4'" C14 C 0 1 N N R N N N ? ? ? -2.931 -1.061 0.525 "C4'" M3X 18 M3X "C5'" C15 C 0 1 N N N N N N ? ? ? -4.458 -1.089 0.618 "C5'" M3X 19 M3X N2 N3 N 0 1 N N N N N N ? ? ? 1.524 0.964 0.042 N2 M3X 20 M3X N3 N4 N 0 1 Y N N N N N ? ? ? 1.034 3.246 -0.028 N3 M3X 21 M3X N4 N5 N 0 1 N N N N N N ? ? ? 0.628 5.567 -0.108 N4 M3X 22 M3X "O2'" O3 O 0 1 N N N N N N ? ? ? 0.125 -0.856 2.086 "O2'" M3X 23 M3X "O3'" O4 O 0 1 N N N N N N ? ? ? -1.901 -2.384 2.303 "O3'" M3X 24 M3X "O4'" O5 O 0 1 N N N N N N ? ? ? -2.485 0.175 -0.074 "O4'" M3X 25 M3X "O5'" O6 O 0 1 N N N N N N ? ? ? -5.013 -1.204 -0.694 "O5'" M3X 26 M3X OP2 O7 O 0 1 N N N N N N ? ? ? -6.863 -1.259 -2.562 OP1 M3X 27 M3X OP3 O8 O 0 1 N Y N N N N ? ? ? -7.207 -2.607 -0.331 OP2 M3X 28 M3X P P1 P 0 1 N N N N N N ? ? ? -6.598 -1.262 -0.974 P M3X 29 M3X H1 H1 H 0 1 N N N N N N ? ? ? -1.907 4.797 0.172 H1 M3X 30 M3X H2 H2 H 0 1 N N N N N N ? ? ? -2.638 2.435 0.358 H2 M3X 31 M3X H3 H3 H 0 1 N N N N N N ? ? ? 8.718 0.126 -1.871 H3 M3X 32 M3X H5 H5 H 0 1 N N N N N N ? ? ? 7.468 -0.767 -2.507 H5 M3X 33 M3X H6 H6 H 0 1 N N N N N N ? ? ? 9.085 -3.367 0.896 H6 M3X 34 M3X H7 H7 H 0 1 N N N N N N ? ? ? 5.861 -1.587 0.649 H7 M3X 35 M3X H8 H8 H 0 1 N N N N N N ? ? ? 5.690 -1.678 -1.120 H8 M3X 36 M3X H9 H9 H 0 1 N N N N N N ? ? ? 5.568 0.874 0.551 H9 M3X 37 M3X H10 H10 H 0 1 N N N N N N ? ? ? 5.397 0.783 -1.218 H10 M3X 38 M3X H11 H11 H 0 1 N N N N N N ? ? ? 3.408 -0.674 -0.951 H11 M3X 39 M3X H12 H12 H 0 1 N N N N N N ? ? ? 3.579 -0.583 0.818 H12 M3X 40 M3X H13 H13 H 0 1 N N N N N N ? ? ? 3.286 1.877 0.720 H13 M3X 41 M3X H14 H14 H 0 1 N N N N N N ? ? ? 3.115 1.786 -1.049 H14 M3X 42 M3X H15 H15 H 0 1 N N N N N N ? ? ? 7.829 -0.058 0.332 H15 M3X 43 M3X H16 H16 H 0 1 N N N N N N ? ? ? -0.465 -0.323 -0.278 H16 M3X 44 M3X H17 H17 H 0 1 N N N N N N ? ? ? -1.171 0.722 2.471 H17 M3X 45 M3X H18 H18 H 0 1 N N N N N N ? ? ? -3.010 -0.663 2.667 H18 M3X 46 M3X H19 H19 H 0 1 N N N N N N ? ? ? -2.571 -1.913 -0.051 H19 M3X 47 M3X H20 H20 H 0 1 N N N N N N ? ? ? -4.770 -1.942 1.220 H20 M3X 48 M3X H21 H21 H 0 1 N N N N N N ? ? ? -4.811 -0.168 1.082 H21 M3X 49 M3X H22 H22 H 0 1 N N N N N N ? ? ? 1.223 0.045 0.118 H22 M3X 50 M3X H23 H23 H 0 1 N N N N N N ? ? ? -0.004 6.302 -0.089 H23 M3X 51 M3X H24 H24 H 0 1 N N N N N N ? ? ? 1.577 5.745 -0.206 H24 M3X 52 M3X H25 H25 H 0 1 N N N N N N ? ? ? 0.195 -1.164 3.000 H25 M3X 53 M3X H26 H26 H 0 1 N N N N N N ? ? ? -1.448 -2.434 3.156 H26 M3X 54 M3X H27 H27 H 0 1 N N N N N N ? ? ? -7.798 -1.293 -2.805 H27 M3X 55 M3X H28 H28 H 0 1 N Y N N N N ? ? ? -6.824 -3.421 -0.686 H28 M3X 56 M3X OP1 O9 O 0 1 N N N N N N ? ? ? -7.251 -0.083 -0.362 O1 M3X 57 # 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 M3X N4 C4 SING N N 1 M3X C4 C5 DOUB Y N 2 M3X C4 N3 SING Y N 3 M3X C5 C6 SING Y N 4 M3X N3 C2 DOUB Y N 5 M3X OP2 P SING N N 6 M3X C6 N1 DOUB Y N 7 M3X P OP3 SING N N 8 M3X P "O5'" SING N N 9 M3X C2 N1 SING Y N 10 M3X C2 N2 SING N N 11 M3X CD CE SING N N 12 M3X CD CG SING N N 13 M3X CE N2 SING N N 14 M3X N1 "C1'" SING N N 15 M3X "O5'" "C5'" SING N N 16 M3X CB CG SING N N 17 M3X CB CZ SING N N 18 M3X OXT C DOUB N N 19 M3X "C1'" "O4'" SING N N 20 M3X "C1'" "C2'" SING N N 21 M3X C CZ SING N N 22 M3X C O SING N N 23 M3X CZ N SING N N 24 M3X "C5'" "C4'" SING N N 25 M3X "O4'" "C4'" SING N N 26 M3X "C3'" "C2'" SING N N 27 M3X "C3'" "C4'" SING N N 28 M3X "C3'" "O3'" SING N N 29 M3X "C2'" "O2'" SING N N 30 M3X C5 H1 SING N N 31 M3X C6 H2 SING N N 32 M3X N H3 SING N N 33 M3X N H5 SING N N 34 M3X O H6 SING N N 35 M3X CB H7 SING N N 36 M3X CB H8 SING N N 37 M3X CG H9 SING N N 38 M3X CG H10 SING N N 39 M3X CD H11 SING N N 40 M3X CD H12 SING N N 41 M3X CE H13 SING N N 42 M3X CE H14 SING N N 43 M3X CZ H15 SING N N 44 M3X "C1'" H16 SING N N 45 M3X "C2'" H17 SING N N 46 M3X "C3'" H18 SING N N 47 M3X "C4'" H19 SING N N 48 M3X "C5'" H20 SING N N 49 M3X "C5'" H21 SING N N 50 M3X N2 H22 SING N N 51 M3X N4 H23 SING N N 52 M3X N4 H24 SING N N 53 M3X "O2'" H25 SING N N 54 M3X "O3'" H26 SING N N 55 M3X OP2 H27 SING N N 56 M3X OP3 H28 SING N N 57 M3X P OP1 DOUB N N 58 # 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 M3X InChI InChI 1.06 "InChI=1S/C15H26N5O9P/c16-8(14(23)24)3-1-2-5-18-15-19-10(17)4-6-20(15)13-12(22)11(21)9(29-13)7-28-30(25,26)27/h4,6,8-9,11-13,21-22H,1-3,5,7,16H2,(H5,17,18,19,23,24,25,26,27)/p+1/t8-,9+,11+,12+,13+/m0/s1" M3X InChIKey InChI 1.06 HXUVGGWPASIJQK-IINAIABHSA-O M3X SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCCCNc1nc(N)cc[n+]1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(O)=O" M3X SMILES CACTVS 3.385 "N[CH](CCCCNc1nc(N)cc[n+]1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(O)=O" M3X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" M3X SMILES "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1N)NCCCCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id M3X _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 "(2~{S})-2-azanyl-6-[[4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-1-ium-2-yl]amino]hexanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id M3X _pdbx_chem_comp_synonyms.name ;lysidine 5'-monophosphate ; _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site M3X "Create component" 2022-12-22 PDBJ M3X "Modify atom id" 2022-12-23 PDBJ M3X "Modify synonyms" 2023-01-06 PDBJ M3X "Initial release" 2024-03-06 RCSB #