data_A1IT3
# 
_chem_comp.id                                    A1IT3 
_chem_comp.name                                  "2'-thiouridine-5'-monophosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N2 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;((2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-4-mercaptotetrahydrofuran-2-yl)methyl dihydrogen phosphate; [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-sulfanyl-oxolan-2-yl]methyl dihydrogen phosphate; 2'-SH UMP
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-13 
_chem_comp.pdbx_modified_date                    2025-10-17 
_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                        340.247 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IT3 
_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        9HDY 
_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 
A1IT3 C4     C1  C 0 1 N N N N N N 17.276 9.654  36.223 4.310  -2.134 -0.015 C4     A1IT3 1  
A1IT3 C5     C2  C 0 1 N N N N N N 16.332 9.490  35.205 4.298  -1.387 1.187  C5     A1IT3 2  
A1IT3 C6     C3  C 0 1 N N N N N N 14.994 9.771  35.456 3.311  -0.489 1.394  C6     A1IT3 3  
A1IT3 N1     N1  N 0 1 N N N N N N 14.652 10.190 36.704 2.342  -0.317 0.443  N1     A1IT3 4  
A1IT3 C2     C4  C 0 1 N N N N N N 15.621 10.364 37.696 2.364  -1.033 -0.696 C2     A1IT3 5  
A1IT3 "C1'"  C5  C 0 1 N N R N N N 13.253 10.455 36.977 1.271  0.657  0.667  "C1'"  A1IT3 6  
A1IT3 "C2'"  C6  C 0 1 N N R N N N 12.708 9.527  38.113 1.312  1.761  -0.412 "C2'"  A1IT3 7  
A1IT3 "C3'"  C7  C 0 1 N N R N N N 11.597 10.415 38.703 -0.176 2.069  -0.692 "C3'"  A1IT3 8  
A1IT3 "C4'"  C8  C 0 1 N N R N N N 12.119 11.849 38.511 -0.940 1.114  0.251  "C4'"  A1IT3 9  
A1IT3 "C5'"  C9  C 0 1 N N N N N N 12.773 12.478 39.723 -2.205 0.591  -0.431 "C5'"  A1IT3 10 
A1IT3 N3     N2  N 0 1 N N N N N N 16.909 10.074 37.443 3.337  -1.934 -0.928 N3     A1IT3 11 
A1IT3 O1P    O1  O 0 1 N N N N N N 10.898 13.266 42.968 -4.979 -1.593 1.429  O1P    A1IT3 12 
A1IT3 O2     O2  O 0 1 N N N N N N 15.326 10.738 38.870 1.493  -0.863 -1.527 O2     A1IT3 13 
A1IT3 O2P    O3  O 0 1 N N N N N N 13.318 12.745 42.870 -4.092 -2.030 -1.007 O2P    A1IT3 14 
A1IT3 "O3'"  O4  O 0 1 N N N N N N 10.362 10.183 38.009 -0.473 3.431  -0.379 "O3'"  A1IT3 15 
A1IT3 O3P    O5  O 0 1 N N N N N N 12.498 14.799 41.794 -5.293 0.108  -0.409 O3P    A1IT3 16 
A1IT3 O4     O6  O 0 1 N N N N N N 18.493 9.449  36.035 5.193  -2.945 -0.227 O4     A1IT3 17 
A1IT3 "O4'"  O7  O 0 1 N N N N N N 13.078 11.819 37.415 -0.020 0.030  0.505  "O4'"  A1IT3 18 
A1IT3 "O5'"  O8  O 0 1 N N N N N N 11.825 12.563 40.813 -2.957 -0.195 0.496  "O5'"  A1IT3 19 
A1IT3 P      P1  P 0 1 N N N N N N 12.155 13.394 42.177 -4.351 -0.905 0.116  P      A1IT3 20 
A1IT3 "S2'"  S1  S 0 1 N N N N N N 12.183 7.962  37.476 2.159  3.236  0.219  "S2'"  A1IT3 21 
A1IT3 H5     H1  H 0 1 N N N N N N 16.641 9.147  34.229 5.069  -1.533 1.929  H5     A1IT3 22 
A1IT3 H6     H2  H 0 1 N N N N N N 14.248 9.660  34.683 3.286  0.089  2.306  H6     A1IT3 23 
A1IT3 "H1'"  H3  H 0 1 N N N N N N 12.657 10.275 36.070 1.358  1.094  1.662  "H1'"  A1IT3 24 
A1IT3 "H2'"  H4  H 0 1 N N N N N N 13.492 9.340  38.861 1.803  1.395  -1.314 "H2'"  A1IT3 25 
A1IT3 "H3'"  H5  H 0 1 N N N N N N 11.490 10.204 39.777 -0.421 1.855  -1.733 "H3'"  A1IT3 26 
A1IT3 "H4'"  H6  H 0 1 N N N N N N 11.267 12.480 38.218 -1.195 1.623  1.181  "H4'"  A1IT3 27 
A1IT3 "H5'2" H7  H 0 0 N N N N N N 13.630 11.863 40.034 -2.811 1.432  -0.769 "H5'2" A1IT3 28 
A1IT3 "H5'1" H8  H 0 0 N N N N N N 13.122 13.489 39.465 -1.928 -0.024 -1.288 "H5'1" A1IT3 29 
A1IT3 HN3    H9  H 0 1 N N N N N N 17.594 10.171 38.165 3.338  -2.441 -1.754 HN3    A1IT3 30 
A1IT3 H1     H10 H 0 1 N N N N N N 10.516 14.126 43.098 -5.821 -2.040 1.275  H1     A1IT3 31 
A1IT3 H2     H11 H 0 1 N N N N N N 14.039 13.361 42.925 -3.482 -2.728 -0.731 H2     A1IT3 32 
A1IT3 "HO3'" H12 H 0 0 N N N N N N 9.682  10.734 38.379 0.026  4.073  -0.903 "HO3'" A1IT3 33 
A1IT3 "HO2'" H13 H 0 0 N N N N N N 11.775 7.356  38.551 2.109  4.083  -0.824 "HO2'" A1IT3 34 
# 
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 
A1IT3 C5    C6     DOUB N N 1  
A1IT3 C5    C4     SING N N 2  
A1IT3 C6    N1     SING N N 3  
A1IT3 O4    C4     DOUB N N 4  
A1IT3 C4    N3     SING N N 5  
A1IT3 N1    "C1'"  SING N N 6  
A1IT3 N1    C2     SING N N 7  
A1IT3 "C1'" "O4'"  SING N N 8  
A1IT3 "C1'" "C2'"  SING N N 9  
A1IT3 "O4'" "C4'"  SING N N 10 
A1IT3 N3    C2     SING N N 11 
A1IT3 "S2'" "C2'"  SING N N 12 
A1IT3 C2    O2     DOUB N N 13 
A1IT3 "O3'" "C3'"  SING N N 14 
A1IT3 "C2'" "C3'"  SING N N 15 
A1IT3 "C4'" "C3'"  SING N N 16 
A1IT3 "C4'" "C5'"  SING N N 17 
A1IT3 "C5'" "O5'"  SING N N 18 
A1IT3 "O5'" P      SING N N 19 
A1IT3 O3P   P      DOUB N N 20 
A1IT3 P     O2P    SING N N 21 
A1IT3 P     O1P    SING N N 22 
A1IT3 C5    H5     SING N N 23 
A1IT3 C6    H6     SING N N 24 
A1IT3 "C1'" "H1'"  SING N N 25 
A1IT3 "C2'" "H2'"  SING N N 26 
A1IT3 "C3'" "H3'"  SING N N 27 
A1IT3 "C4'" "H4'"  SING N N 28 
A1IT3 "C5'" "H5'2" SING N N 29 
A1IT3 "C5'" "H5'1" SING N N 30 
A1IT3 N3    HN3    SING N N 31 
A1IT3 O1P   H1     SING N N 32 
A1IT3 O2P   H2     SING N N 33 
A1IT3 "O3'" "HO3'" SING N N 34 
A1IT3 "S2'" "HO2'" SING N N 35 
# 
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 
A1IT3 InChI            InChI                1.06  "InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(14)10-5)8-7(21)6(13)4(19-8)3-18-20(15,16)17/h1-2,4,6-8,13,21H,3H2,(H,10,12,14)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1" 
A1IT3 InChIKey         InChI                1.06  NYWGEABRDXTLQJ-XVFCMESISA-N                                                                                                                          
A1IT3 SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](S)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                       
A1IT3 SMILES           CACTVS               3.385 "O[CH]1[CH](S)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                              
A1IT3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)S"                                                                                      
A1IT3 SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)S"                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           A1IT3 
_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~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-sulfanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 A1IT3 "((2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-4-mercaptotetrahydrofuran-2-yl)methyl dihydrogen phosphate"   AUTHOR ? 
2 A1IT3 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-sulfanyl-oxolan-2-yl]methyl dihydrogen phosphate" PDB    ? 
3 A1IT3 
;2'-SH UMP
;
AUTHOR ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1IT3 "Create component" 2024-11-13 PDBE 
A1IT3 "Initial release"  2025-10-22 RCSB 
# 
