data_YTI
# 
_chem_comp.id                                    YTI 
_chem_comp.name                                  "(3R,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-20 
_chem_comp.pdbx_modified_date                    2024-08-23 
_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                        292.182 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YTI 
_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        8T3X 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
YTI P     P1  P 0 1 N N N N N N 12.109 11.249 4.358  4.108  0.125  -0.375 P     YTI 1  
YTI O1P   O1  O 0 1 N N N N N N 12.906 11.964 3.328  4.735  -0.382 0.866  O1P   YTI 2  
YTI O2P   O2  O 0 1 N N N N N N 11.739 12.185 5.437  4.246  -0.981 -1.537 O2P   YTI 3  
YTI "C4'" C1  C 0 1 N N N N N N 11.035 8.223  3.764  1.003  -0.065 1.740  "C4'" YTI 4  
YTI "O4'" O3  O 0 1 N N N N N N 10.260 7.216  4.710  -0.248 -0.765 1.826  "O4'" YTI 5  
YTI "C3'" C2  C 0 1 N N R N N N 10.059 9.469  3.717  1.647  -0.549 0.416  "C3'" YTI 6  
YTI "O3'" O4  O 0 1 N N N N N N 10.743 10.748 3.637  2.550  0.428  -0.105 "O3'" YTI 7  
YTI "C2'" C3  C 0 1 N N N N N N 9.234  9.395  4.819  0.392  -0.690 -0.488 "C2'" YTI 8  
YTI "C1'" C4  C 0 1 N N R N N N 9.021  7.991  5.033  -0.687 -1.147 0.517  "C1'" YTI 9  
YTI N1    N1  N 0 1 N N N N N N 8.676  7.733  6.416  -1.962 -0.495 0.209  N1    YTI 10 
YTI C2    C5  C 0 1 N N N N N N 8.102  6.424  6.747  -2.071 0.842  0.323  C2    YTI 11 
YTI O2    O5  O 0 1 N N N N N N 7.931  5.619  5.883  -1.108 1.493  0.680  O2    YTI 12 
YTI N3    N2  N 0 1 N N N N N N 7.758  6.129  8.104  -3.230 1.467  0.047  N3    YTI 13 
YTI C4    C6  C 0 1 N N N N N N 7.980  7.101  9.118  -4.306 0.759  -0.350 C4    YTI 14 
YTI O4    O6  O 0 1 N N N N N N 7.710  6.889  10.271 -5.356 1.324  -0.601 O4    YTI 15 
YTI C5    C7  C 0 1 N N N N N N 8.581  8.458  8.769  -4.205 -0.647 -0.474 C5    YTI 16 
YTI C6    C8  C 0 1 N N N N N N 8.912  8.747  7.476  -3.029 -1.249 -0.196 C6    YTI 17 
YTI C5M   C9  C 0 1 N N N N N N 8.770  9.475  9.936  -5.393 -1.462 -0.917 C5M   YTI 18 
YTI H2    H2  H 0 1 N N N N N N 12.089 13.047 5.243  3.856  -0.716 -2.381 H2    YTI 19 
YTI H3    H3  H 0 1 N N N N N N 11.181 7.794  2.762  0.833  1.011  1.706  H3    YTI 20 
YTI H4    H4  H 0 1 N N N N N N 12.011 8.498  4.191  1.639  -0.321 2.587  H4    YTI 21 
YTI H5    H5  H 0 1 N N N N N N 9.451  9.353  2.808  2.144  -1.510 0.550  H5    YTI 22 
YTI H6    H6  H 0 1 N N N N N N 9.718  9.850  5.695  0.126  0.269  -0.933 H6    YTI 23 
YTI H7    H7  H 0 1 N N N N N N 8.279  9.905  4.622  0.551  -1.445 -1.258 H7    YTI 24 
YTI H8    H8  H 0 1 N N N N N N 8.206  7.640  4.383  -0.803 -2.230 0.467  H8    YTI 25 
YTI H9    H9  H 0 1 N N N N N N 7.362  5.241  8.339  -3.291 2.431  0.135  H9    YTI 26 
YTI H10   H10 H 0 1 N N N N N N 9.342  9.706  7.226  -2.931 -2.320 -0.290 H10   YTI 27 
YTI H11   H11 H 0 1 N N N N N N 8.435  9.018  10.879 -6.241 -0.801 -1.097 H11   YTI 28 
YTI H12   H12 H 0 1 N N N N N N 9.833  9.746  10.018 -5.147 -1.995 -1.836 H12   YTI 29 
YTI H13   H13 H 0 1 N N N N N N 8.176  10.378 9.735  -5.651 -2.181 -0.139 H13   YTI 30 
YTI O3P   O3P O 0 1 N Y N N N N 13.093 10.146 4.977  4.846  1.480  -0.835 O3P   YTI 31 
YTI H3P   H3P H 0 1 N Y N N N N 13.941 10.203 4.552  5.790  1.373  -1.015 H3P   YTI 32 
# 
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 
YTI O1P   P     DOUB N N 1  
YTI "O3'" "C3'" SING N N 2  
YTI "O3'" P     SING N N 3  
YTI "C3'" "C4'" SING N N 4  
YTI "C3'" "C2'" SING N N 5  
YTI "C4'" "O4'" SING N N 6  
YTI P     O2P   SING N N 7  
YTI "O4'" "C1'" SING N N 8  
YTI "C2'" "C1'" SING N N 9  
YTI "C1'" N1    SING N N 10 
YTI O2    C2    DOUB N N 11 
YTI N1    C2    SING N N 12 
YTI N1    C6    SING N N 13 
YTI C2    N3    SING N N 14 
YTI C6    C5    DOUB N N 15 
YTI N3    C4    SING N N 16 
YTI C5    C4    SING N N 17 
YTI C5    C5M   SING N N 18 
YTI C4    O4    DOUB N N 19 
YTI O2P   H2    SING N N 20 
YTI "C4'" H3    SING N N 21 
YTI "C4'" H4    SING N N 22 
YTI "C3'" H5    SING N N 23 
YTI "C2'" H6    SING N N 24 
YTI "C2'" H7    SING N N 25 
YTI "C1'" H8    SING N N 26 
YTI N3    H9    SING N N 27 
YTI C6    H10   SING N N 28 
YTI C5M   H11   SING N N 29 
YTI C5M   H12   SING N N 30 
YTI C5M   H13   SING N N 31 
YTI P     O3P   SING N N 32 
YTI O3P   H3P   SING N N 33 
# 
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 
YTI SMILES           ACDLabs              12.01 "O=P(O)(O)OC1COC(C1)N1C=C(C)C(=O)NC1=O"                                                                                             
YTI InChI            InChI                1.06  "InChI=1S/C9H13N2O7P/c1-5-3-11(9(13)10-8(5)12)7-2-6(4-17-7)18-19(14,15)16/h3,6-7H,2,4H2,1H3,(H,10,12,13)(H2,14,15,16)/t6-,7-/m1/s1" 
YTI InChIKey         InChI                1.06  KKIOPTSGYFLUCQ-RNFRBKRXSA-N                                                                                                         
YTI SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](CO2)O[P](O)(O)=O)C(=O)NC1=O"                                                                                   
YTI SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](CO2)O[P](O)(O)=O)C(=O)NC1=O"                                                                                     
YTI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@H](CO2)OP(=O)(O)O"                                                                                     
YTI SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(CO2)OP(=O)(O)O"                                                                                             
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
YTI "SYSTEMATIC NAME" ACDLabs              12.01 "(3R,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate"      
YTI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-3-yl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YTI "Create component" 2023-06-21 RCSB 
YTI "Initial release"  2024-08-28 RCSB 
# 
