data_A1I9V # _chem_comp.id A1I9V _chem_comp.name "5-METHYL-2-THIO-URIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms "[(2~{R},3~{S},4~{R},5~{R})-5-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-04-04 _chem_comp.pdbx_modified_date 2025-12-02 _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 354.273 _chem_comp.one_letter_code U _chem_comp.three_letter_code A1I9V _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 9QRP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1I9V P P1 P 0 1 N N N N N N 49.807 -51.728 -0.093 4.293 -1.022 -0.250 P A1I9V 1 A1I9V OP1 O1 O 0 1 N N N N N N 50.133 -50.576 -0.962 5.370 -0.125 0.223 OP1 A1I9V 2 A1I9V OP3 O2 O 0 1 N N N N N N 50.384 -51.804 1.268 3.892 -2.047 0.925 OP2 A1I9V 3 A1I9V "O5'" O3 O 0 1 N N N N N N 50.214 -53.056 -0.875 3.006 -0.146 -0.660 "O5'" A1I9V 4 A1I9V N1 N1 N 0 1 N N N N N N 50.796 -54.896 -4.510 -2.173 0.167 -0.349 N1 A1I9V 5 A1I9V C6 C1 C 0 1 N N N N N N 50.423 -53.597 -4.224 -3.278 0.149 -1.155 C6 A1I9V 6 A1I9V C2 C2 C 0 1 N N N N N N 51.281 -55.246 -5.758 -2.058 -0.698 0.675 C2 A1I9V 7 A1I9V N3 N2 N 0 1 N N N N N N 51.353 -54.216 -6.665 -3.027 -1.596 0.935 N3 A1I9V 8 A1I9V C4 C3 C 0 1 N N N N N N 50.994 -52.898 -6.451 -4.134 -1.641 0.168 C4 A1I9V 9 A1I9V O4 O4 O 0 1 N N N N N N 51.108 -52.075 -7.352 -5.011 -2.453 0.402 O4 A1I9V 10 A1I9V C5 C4 C 0 1 N N N N N N 50.503 -52.613 -5.129 -4.263 -0.744 -0.920 C5 A1I9V 11 A1I9V "C2'" C5 C 0 1 N N R N N N 52.043 -56.220 -2.799 -0.899 2.063 0.616 "C2'" A1I9V 12 A1I9V "C5'" C6 C 0 1 N N N N N N 49.928 -54.336 -0.330 2.378 0.778 0.230 "C5'" A1I9V 13 A1I9V "C4'" C7 C 0 1 N N R N N N 50.493 -55.448 -1.181 1.190 1.438 -0.474 "C4'" A1I9V 14 A1I9V "O4'" O5 O 0 1 N N N N N N 49.804 -55.496 -2.457 0.170 0.459 -0.733 "O4'" A1I9V 15 A1I9V "C1'" C8 C 0 1 N N R N N N 50.692 -55.939 -3.464 -1.102 1.132 -0.607 "C1'" A1I9V 16 A1I9V "C3'" C9 C 0 1 N N S N N N 51.959 -55.326 -1.568 0.571 2.514 0.440 "C3'" A1I9V 17 A1I9V "O3'" O6 O 0 1 N N N N N N 52.848 -55.702 -0.528 0.629 3.796 -0.188 "O3'" A1I9V 18 A1I9V "O2'" O7 O 0 1 N N N N N N 52.078 -57.589 -2.420 -1.786 3.181 0.558 "O2'" A1I9V 19 A1I9V C5M C10 C 0 1 N N N N N N 50.073 -51.232 -4.732 -5.491 -0.774 -1.794 C5M A1I9V 20 A1I9V S2 S1 S 0 1 N N N N N N 51.647 -56.457 -6.069 -0.659 -0.657 1.661 S2 A1I9V 21 A1I9V OP2 O8 O 0 1 N Y N N N N 48.205 -51.816 0.026 4.808 -1.850 -1.531 O1 A1I9V 22 A1I9V HOP3 H1 H 0 1 N N N N N N 50.933 -51.044 1.423 3.190 -2.667 0.684 H1 A1I9V 23 A1I9V H6 H2 H 0 1 N N N N N N 50.054 -53.367 -3.236 -3.363 0.847 -1.974 H2 A1I9V 24 A1I9V H3 H3 H 0 1 N N N N N N 51.701 -54.443 -7.574 -2.928 -2.212 1.678 H3 A1I9V 25 A1I9V "H2'" H4 H 0 1 N N N N N N 52.880 -55.930 -3.452 -1.028 1.514 1.548 H4 A1I9V 26 A1I9V "H5'" H5 H 0 1 N N N N N N 48.837 -54.458 -0.263 2.026 0.248 1.116 H5 A1I9V 27 A1I9V "H5''" H6 H 0 1 N N N N N N 50.367 -54.400 0.677 3.096 1.543 0.525 H6 A1I9V 28 A1I9V "H4'" H7 H 0 1 N N N N N N 50.350 -56.402 -0.652 1.518 1.888 -1.411 H7 A1I9V 29 A1I9V "H1'" H8 H 0 1 N N N N N N 50.322 -56.871 -3.915 -1.320 1.715 -1.502 H8 A1I9V 30 A1I9V "H3'" H9 H 0 1 N N N N N N 52.156 -54.288 -1.875 1.082 2.536 1.403 H9 A1I9V 31 A1I9V "HO3'" H10 H 0 1 N Y N N N N 52.746 -55.108 0.206 0.202 4.501 0.317 H10 A1I9V 32 A1I9V "HO2'" H11 H 0 1 N N N N N N 52.910 -57.782 -2.005 -1.637 3.838 1.252 H11 A1I9V 33 A1I9V "HM'" H12 H 0 1 N N N N N N 49.735 -51.239 -3.685 -6.170 -1.549 -1.439 H12 A1I9V 34 A1I9V HM H13 H 0 1 N N N N N N 50.921 -50.539 -4.839 -5.990 0.194 -1.752 H13 A1I9V 35 A1I9V "HM''" H14 H 0 1 N N N N N N 49.248 -50.904 -5.381 -5.200 -0.989 -2.822 H14 A1I9V 36 A1I9V HOP2 H15 H 0 1 N N N N N N 47.810 -51.117 -0.482 5.583 -2.402 -1.357 H15 A1I9V 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 A1I9V P "O5'" SING N N 1 A1I9V P OP1 DOUB N N 2 A1I9V P OP3 SING N N 3 A1I9V "C1'" "C2'" SING N N 4 A1I9V "C2'" "C3'" SING N N 5 A1I9V "C3'" "C4'" SING N N 6 A1I9V "C3'" "O3'" SING N N 7 A1I9V "C4'" "C5'" SING N N 8 A1I9V "C4'" "O4'" SING N N 9 A1I9V "O4'" "C1'" SING N N 10 A1I9V "C5'" "O5'" SING N N 11 A1I9V "C2'" "O2'" SING N N 12 A1I9V N1 C2 SING N N 13 A1I9V C2 N3 SING N N 14 A1I9V N3 C4 SING N N 15 A1I9V C4 C5 SING N N 16 A1I9V C5 C6 DOUB N N 17 A1I9V C6 N1 SING N N 18 A1I9V C2 S2 DOUB N N 19 A1I9V C4 O4 DOUB N N 20 A1I9V N1 "C1'" SING N N 21 A1I9V C5M C5 SING N N 22 A1I9V P OP2 SING N N 23 A1I9V OP3 HOP3 SING N N 24 A1I9V C6 H6 SING N N 25 A1I9V N3 H3 SING N N 26 A1I9V "C2'" "H2'" SING N N 27 A1I9V "C5'" "H5'" SING N N 28 A1I9V "C5'" "H5''" SING N N 29 A1I9V "C4'" "H4'" SING N N 30 A1I9V "C1'" "H1'" SING N N 31 A1I9V "C3'" "H3'" SING N N 32 A1I9V "O3'" "HO3'" SING N N 33 A1I9V "O2'" "HO2'" SING N N 34 A1I9V C5M "HM'" SING N N 35 A1I9V C5M HM SING N N 36 A1I9V C5M "HM''" SING N N 37 A1I9V OP2 HOP2 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 A1I9V InChI InChI 1.06 "InChI=1S/C10H15N2O8PS/c1-4-2-12(10(22)11-8(4)15)9-7(14)6(13)5(20-9)3-19-21(16,17)18/h2,5-7,9,13-14H,3H2,1H3,(H,11,15,22)(H2,16,17,18)/t5-,6-,7-,9-/m1/s1" A1I9V InChIKey InChI 1.06 TYPPXSBSSBTYPX-JXOAFFINSA-N A1I9V SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=S)NC1=O" A1I9V SMILES CACTVS 3.385 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=S)NC1=O" A1I9V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=S)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" A1I9V SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=S)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1I9V _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-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1I9V _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},4~{R},5~{R})-5-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _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 A1I9V "Create component" 2025-04-04 PDBE A1I9V "Initial release" 2025-05-14 RCSB A1I9V "Modify atom id" 2025-12-02 PDBE #