data_7S3 # _chem_comp.id 7S3 _chem_comp.name "[(2R,3S,4R,5R)-5-(1-methyl-6-oxidanylidene-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms "1-methyl inosinic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-10-15 _chem_comp.pdbx_modified_date 2022-06-08 _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 362.233 _chem_comp.one_letter_code G _chem_comp.three_letter_code 7S3 _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 7VNV _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.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 7S3 C2 C1 C 0 1 N N N -138.486 30.583 34.381 4.882 0.749 0.786 C2 7S3 1 7S3 C4 C2 C 0 1 Y N N -140.442 29.581 34.210 2.791 -0.038 0.221 C4 7S3 2 7S3 "C1'" C3 C 0 1 N N R -141.707 28.462 32.299 0.431 0.853 0.377 "C1'" 7S3 3 7S3 "C2'" C4 C 0 1 N N R -141.083 27.114 31.952 0.238 1.852 -0.792 "C2'" 7S3 4 7S3 "C3'" C5 C 0 1 N N S -142.280 26.186 32.084 -1.199 2.369 -0.543 "C3'" 7S3 5 7S3 "C4'" C6 C 0 1 N N R -143.429 27.044 31.584 -1.844 1.283 0.339 "C4'" 7S3 6 7S3 C5 C7 C 0 1 Y N N -140.735 29.810 35.541 3.349 -1.231 -0.249 C5 7S3 7 7S3 "C5'" C8 C 0 1 N N N -144.796 26.652 32.088 -3.088 0.718 -0.350 "C5'" 7S3 8 7S3 C6 C9 C 0 1 N N N -139.783 30.517 36.306 4.756 -1.391 -0.179 C6 7S3 9 7S3 C8 C10 C 0 1 Y N N -142.411 28.761 34.735 1.206 -1.369 -0.533 C8 7S3 10 7S3 CM1 C11 C 0 1 N N N -137.573 31.623 36.374 6.943 -0.516 0.447 CM1 7S3 11 7S3 N1 N1 N 0 1 N N N -138.640 30.898 35.679 5.487 -0.384 0.348 N1 7S3 12 7S3 N3 N2 N 0 1 N N N -139.319 29.931 33.558 3.590 0.913 0.724 N3 7S3 13 7S3 N7 N3 N 0 1 Y N N -141.988 29.289 35.859 2.332 -2.003 -0.696 N7 7S3 14 7S3 N9 N4 N 0 1 Y N N -141.522 28.880 33.702 1.441 -0.152 0.035 N9 7S3 15 7S3 "O2'" O1 O 0 1 N N N -140.677 27.179 30.593 1.186 2.919 -0.712 "O2'" 7S3 16 7S3 "O3'" O2 O 0 1 N N N -142.147 25.007 31.322 -1.168 3.622 0.144 "O3'" 7S3 17 7S3 "O4'" O3 O 0 1 N N N -143.094 28.380 32.032 -0.868 0.241 0.519 "O4'" 7S3 18 7S3 "O5'" O4 O 0 1 N N N -144.787 26.490 33.501 -3.734 -0.211 0.522 "O5'" 7S3 19 7S3 O6 O5 O 0 1 N N N -139.960 30.776 37.513 5.290 -2.412 -0.575 O6 7S3 20 7S3 OP1 O6 O 0 1 N N N -146.813 25.095 33.714 -6.122 -0.027 -0.274 OP1 7S3 21 7S3 OP2 O7 O 0 1 N N N -145.918 26.345 35.777 -4.774 -1.990 -1.111 OP2 7S3 22 7S3 P P1 P 0 1 N N N -146.144 26.297 34.304 -5.080 -1.000 0.121 P 7S3 23 7S3 OP3 O8 O 0 1 N Y N -147.050 27.554 33.864 -5.596 -1.857 1.383 OP3 7S3 24 7S3 "H1'" H1 H 0 1 N N N -137.555 30.902 33.937 5.489 1.538 1.203 "H1'" 7S3 25 7S3 H1 H2 H 0 1 N N N -141.254 29.222 31.645 0.709 1.380 1.290 H1 7S3 26 7S3 "H2'" H3 H 0 1 N N N -140.272 26.844 32.644 0.308 1.344 -1.754 "H2'" 7S3 27 7S3 "H3'" H4 H 0 1 N N N -142.440 25.949 33.146 -1.739 2.466 -1.485 "H3'" 7S3 28 7S3 "H4'" H5 H 0 1 N N N -143.436 27.015 30.484 -2.114 1.709 1.306 "H4'" 7S3 29 7S3 "H5'" H6 H 0 1 N N N -145.518 27.437 31.820 -3.774 1.532 -0.585 "H5'" 7S3 30 7S3 "H5''" H7 H 0 0 N N N -145.095 25.703 31.618 -2.796 0.211 -1.269 "H5''" 7S3 31 7S3 H8 H8 H 0 1 N N N -143.371 28.277 34.635 0.233 -1.751 -0.803 H8 7S3 32 7S3 H9 H9 H 0 1 N N N -137.867 31.795 37.420 7.360 0.387 0.893 H9 7S3 33 7S3 H10 H10 H 0 1 N N N -136.648 31.029 36.346 7.189 -1.375 1.070 H10 7S3 34 7S3 H11 H11 H 0 1 N N N -137.403 32.590 35.878 7.364 -0.656 -0.549 H11 7S3 35 7S3 "HO2'" H12 H 0 0 N N N -139.929 27.759 30.513 1.049 3.616 -1.369 "HO2'" 7S3 36 7S3 "HO3'" H13 H 0 0 N N N -141.422 24.493 31.658 -0.721 4.327 -0.344 "HO3'" 7S3 37 7S3 HOP2 H14 H 0 0 N N N -146.252 25.550 36.175 -4.099 -2.655 -0.923 HOP2 7S3 38 7S3 HOP3 H15 H 0 0 N Y N -147.784 27.249 33.343 -6.405 -2.359 1.213 HOP3 7S3 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 7S3 "O2'" "C2'" SING N N 1 7S3 "O3'" "C3'" SING N N 2 7S3 "C4'" "O4'" SING N N 3 7S3 "C4'" "C3'" SING N N 4 7S3 "C4'" "C5'" SING N N 5 7S3 "C2'" "C3'" SING N N 6 7S3 "C2'" "C1'" SING N N 7 7S3 "O4'" "C1'" SING N N 8 7S3 "C5'" "O5'" SING N N 9 7S3 "C1'" N9 SING N N 10 7S3 "O5'" P SING N N 11 7S3 N3 C4 SING N N 12 7S3 N3 C2 DOUB N N 13 7S3 N9 C4 SING Y N 14 7S3 N9 C8 SING Y N 15 7S3 OP1 P DOUB N N 16 7S3 C4 C5 DOUB Y N 17 7S3 P OP2 SING N N 18 7S3 C2 N1 SING N N 19 7S3 C8 N7 DOUB Y N 20 7S3 C5 N7 SING Y N 21 7S3 C5 C6 SING N N 22 7S3 N1 C6 SING N N 23 7S3 N1 CM1 SING N N 24 7S3 C6 O6 DOUB N N 25 7S3 P OP3 SING N N 26 7S3 C2 "H1'" SING N N 27 7S3 "C1'" H1 SING N N 28 7S3 "C2'" "H2'" SING N N 29 7S3 "C3'" "H3'" SING N N 30 7S3 "C4'" "H4'" SING N N 31 7S3 "C5'" "H5'" SING N N 32 7S3 "C5'" "H5''" SING N N 33 7S3 C8 H8 SING N N 34 7S3 CM1 H9 SING N N 35 7S3 CM1 H10 SING N N 36 7S3 CM1 H11 SING N N 37 7S3 "O2'" "HO2'" SING N N 38 7S3 "O3'" "HO3'" SING N N 39 7S3 OP2 HOP2 SING N N 40 7S3 OP3 HOP3 SING N N 41 # 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 7S3 InChI InChI 1.03 "InChI=1S/C11H15N4O8P/c1-14-3-13-9-6(10(14)18)12-4-15(9)11-8(17)7(16)5(23-11)2-22-24(19,20)21/h3-5,7-8,11,16-17H,2H2,1H3,(H2,19,20,21)/t5-,7-,8-,11-/m1/s1" 7S3 InChIKey InChI 1.03 CPKNFRPSNBOHIM-IOSLPCCCSA-N 7S3 SMILES_CANONICAL CACTVS 3.385 "CN1C=Nc2n(cnc2C1=O)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" 7S3 SMILES CACTVS 3.385 "CN1C=Nc2n(cnc2C1=O)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" 7S3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C1=O" 7S3 SMILES "OpenEye OEToolkits" 2.0.7 "CN1C=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C1=O" # _pdbx_chem_comp_identifier.comp_id 7S3 _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~{R},3~{S},4~{R},5~{R})-5-(1-methyl-6-oxidanylidene-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 7S3 _pdbx_chem_comp_synonyms.name "1-methyl inosinic acid" _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 7S3 "Create component" 2021-10-15 PDBJ 7S3 "Initial release" 2022-05-04 RCSB 7S3 "Modify parent residue" 2022-06-08 PDBJ #