data_TT9
# 
_chem_comp.id                                    TT9 
_chem_comp.name                                  "[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-2-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 N3 O11 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-29 
_chem_comp.pdbx_modified_date                    2024-04-19 
_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                        435.241 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     TT9 
_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        8J5G 
_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.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 
TT9 N1  N1  N 0 1 N N N N N N 16.524 13.970 2.770  -3.536 -0.192 -0.284 N1  TT9 1  
TT9 N3  N2  N 0 1 N N N N N N 19.692 11.857 0.966  -6.227 -3.253 -0.109 N3  TT9 2  
TT9 C4  C1  C 0 1 N N R N N N 15.481 14.660 3.514  -2.546 0.887  -0.320 C4  TT9 3  
TT9 C5  C2  C 0 1 N N N N N N 17.590 13.401 3.484  -3.315 -1.278 0.480  C5  TT9 4  
TT9 C6  C3  C 0 1 N N N N N N 18.624 12.566 1.590  -5.322 -2.219 -0.171 C6  TT9 5  
TT9 C7  C4  C 0 1 N N N N N N 17.460 13.171 0.769  -5.588 -1.091 -0.974 C7  TT9 6  
TT9 C8  C5  C 0 1 N N N N N N 16.480 13.818 1.362  -4.678 -0.089 -1.020 C8  TT9 7  
TT9 C1  C6  C 0 1 N N S N N N 13.123 15.765 3.111  0.090  1.533  -0.057 C1  TT9 8  
TT9 C2  C7  C 0 1 N N S N N N 14.134 16.630 3.824  -0.819 2.065  1.064  C2  TT9 9  
TT9 C3  C8  C 0 1 N N R N N N 15.445 16.146 3.236  -2.169 1.348  1.112  C3  TT9 10 
TT9 C9  C9  C 0 1 N N N N N N 11.782 15.684 3.813  0.475  2.664  -1.012 C9  TT9 11 
TT9 N2  N3  N 0 1 N N N N N N 18.650 12.692 2.855  -4.199 -2.273 0.532  N2  TT9 12 
TT9 O1  O1  O 0 1 N N N N N N 9.414  18.919 0.604  5.682  -1.498 1.578  O1  TT9 13 
TT9 O10 O2  O 0 1 N N N N N N 17.627 13.528 4.833  -2.289 -1.351 1.136  O10 TT9 14 
TT9 O11 O3  O 0 1 N N N N N N 11.173 16.943 3.815  1.172  3.681  -0.290 O11 TT9 15 
TT9 O2  O4  O 0 1 N N N N N N 11.251 20.269 0.264  5.435  -1.151 -0.910 O2  TT9 16 
TT9 O3  O5  O 0 1 N N N N N N 11.078 19.027 2.233  4.050  -2.979 0.144  O3  TT9 17 
TT9 O4  O6  O 0 1 N N N N N N 11.616 17.725 0.004  3.505  -0.439 0.552  O4  TT9 18 
TT9 O5  O7  O 0 1 N N N N N N 11.306 15.221 0.757  3.113  1.365  -1.320 O5  TT9 19 
TT9 O6  O8  O 0 1 N N N N N N 13.177 15.838 -0.424 1.795  -0.788 -1.272 O6  TT9 20 
TT9 O7  O9  O 0 1 N N N N N N 13.127 16.534 1.942  1.262  0.932  0.497  O7  TT9 21 
TT9 O8  O10 O 0 1 N N N N N N 14.095 16.515 5.219  -1.043 3.461  0.854  O8  TT9 22 
TT9 O9  O11 O 0 1 N N N N N N 16.539 16.787 3.823  -3.168 2.241  1.608  O9  TT9 23 
TT9 P1  P1  P 0 1 N N N N N N 10.863 18.969 0.790  4.685  -1.509 0.314  P1  TT9 24 
TT9 P2  P2  P 0 1 N N N N N N 12.255 16.316 0.595  2.405  0.245  -0.405 P2  TT9 25 
TT9 S1  S1  S 0 1 N N N N N N 13.818 14.067 3.019  -0.921 0.277  -0.930 S1  TT9 26 
TT9 H1  H1  H 0 1 N N N N N N 20.431 11.477 1.521  -6.044 -4.025 0.449  H1  TT9 27 
TT9 H2  H2  H 0 1 N N N N N N 19.702 11.740 -0.027 -7.048 -3.211 -0.625 H2  TT9 28 
TT9 H3  H3  H 0 1 N N N N N N 15.574 14.475 4.594  -2.903 1.724  -0.921 H3  TT9 29 
TT9 H4  H4  H 0 1 N N N N N N 17.452 13.061 -0.305 -6.500 -1.030 -1.549 H4  TT9 30 
TT9 H5  H5  H 0 1 N N N N N N 15.660 14.224 0.788  -4.856 0.782  -1.633 H5  TT9 31 
TT9 H6  H6  H 0 1 N N N N N N 13.978 17.677 3.523  -0.315 1.930  2.021  H6  TT9 32 
TT9 H7  H7  H 0 1 N N N N N N 15.434 16.310 2.148  -2.096 0.481  1.768  H7  TT9 33 
TT9 H8  H8  H 0 1 N N N N N N 11.136 14.967 3.286  1.118  2.272  -1.800 H8  TT9 34 
TT9 H9  H9  H 0 1 N N N N N N 11.932 15.349 4.850  -0.427 3.087  -1.456 H9  TT9 35 
TT9 H10 H10 H 0 1 N N N N N N 9.118  19.726 0.200  6.419  -2.119 1.503  H10 TT9 36 
TT9 H11 H11 H 0 1 N N N N N N 10.333 16.888 4.256  1.447  4.431  -0.835 H11 TT9 37 
TT9 H12 H12 H 0 1 N N N N N N 11.412 19.884 2.470  3.543  -3.279 0.910  H12 TT9 38 
TT9 H13 H13 H 0 1 N N N N N N 11.538 14.511 0.171  3.534  2.075  -0.817 H13 TT9 39 
TT9 H14 H14 H 0 1 N N N N N N 14.753 17.083 5.603  -1.609 3.873  1.521  H14 TT9 40 
TT9 H15 H15 H 0 1 N N N N N N 16.498 17.718 3.637  -4.048 1.847  1.679  H15 TT9 41 
# 
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 
TT9 O6  P2  DOUB N N 1  
TT9 O4  P2  SING N N 2  
TT9 O4  P1  SING N N 3  
TT9 O2  P1  DOUB N N 4  
TT9 P2  O5  SING N N 5  
TT9 P2  O7  SING N N 6  
TT9 O1  P1  SING N N 7  
TT9 C7  C8  DOUB N N 8  
TT9 C7  C6  SING N N 9  
TT9 P1  O3  SING N N 10 
TT9 N3  C6  SING N N 11 
TT9 C8  N1  SING N N 12 
TT9 C6  N2  DOUB N N 13 
TT9 O7  C1  SING N N 14 
TT9 N1  C5  SING N N 15 
TT9 N1  C4  SING N N 16 
TT9 N2  C5  SING N N 17 
TT9 S1  C1  SING N N 18 
TT9 S1  C4  SING N N 19 
TT9 C1  C9  SING N N 20 
TT9 C1  C2  SING N N 21 
TT9 C3  C4  SING N N 22 
TT9 C3  O9  SING N N 23 
TT9 C3  C2  SING N N 24 
TT9 C5  O10 DOUB N N 25 
TT9 C9  O11 SING N N 26 
TT9 C2  O8  SING N N 27 
TT9 N3  H1  SING N N 28 
TT9 N3  H2  SING N N 29 
TT9 C4  H3  SING N N 30 
TT9 C7  H4  SING N N 31 
TT9 C8  H5  SING N N 32 
TT9 C2  H6  SING N N 33 
TT9 C3  H7  SING N N 34 
TT9 C9  H8  SING N N 35 
TT9 C9  H9  SING N N 36 
TT9 O1  H10 SING N N 37 
TT9 O11 H11 SING N N 38 
TT9 O3  H12 SING N N 39 
TT9 O5  H13 SING N N 40 
TT9 O8  H14 SING N N 41 
TT9 O9  H15 SING N N 42 
# 
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 
TT9 InChI            InChI                1.06  "InChI=1S/C9H15N3O11P2S/c10-4-1-2-12(8(16)11-4)7-5(14)6(15)9(3-13,26-7)22-25(20,21)23-24(17,18)19/h1-2,5-7,13-15H,3H2,(H,20,21)(H2,10,11,16)(H2,17,18,19)/t5-,6+,7-,9+/m1/s1" 
TT9 InChIKey         InChI                1.06  KEAXZHZTGMHPPH-AYHNYZOXSA-N                                                                                                                                                   
TT9 SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2S[C@](CO)(O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                                  
TT9 SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2S[C](CO)(O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"                                                                                                        
TT9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@@](S2)(CO)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                   
TT9 SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(S2)(CO)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           TT9 
_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~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-2-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl] phosphono hydrogen 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 
TT9 "Create component" 2023-04-29 PDBJ 
TT9 "Initial release"  2024-04-24 RCSB 
# 
