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 
# 
