data_A1EJD
# 
_chem_comp.id                                    A1EJD 
_chem_comp.name                                  "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-diphosphonooxy-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 N2 O15 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "3h-Uridine tri-phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-01-14 
_chem_comp.pdbx_modified_date                    2025-11-07 
_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                        484.141 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EJD 
_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        9LDH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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 
A1EJD C4  C1  C 0 1 N N N N N N 44.156 -3.322 4.620  -2.384 3.049  1.016  C4  A1EJD 1  
A1EJD C6  C2  C 0 1 N N R N N N 42.232 -4.716 3.880  -0.808 1.174  0.964  C6  A1EJD 2  
A1EJD C8  C3  C 0 1 N N R N N N 43.295 -6.210 2.450  1.149  -0.034 0.689  C8  A1EJD 3  
A1EJD C15 C4  C 0 1 N N R N N N 42.190 -5.500 1.672  0.103  -0.767 -0.196 C15 A1EJD 4  
A1EJD C21 C5  C 0 1 N N R N N N 42.112 -4.193 2.450  -1.228 -0.152 0.300  C21 A1EJD 5  
A1EJD C2  C6  C 0 1 N N N N N N 44.200 -2.352 6.822  -2.722 4.365  -0.945 C2  A1EJD 6  
A1EJD C27 C7  C 0 1 N N N N N N 42.246 -3.622 6.048  -1.222 2.574  -0.980 C27 A1EJD 7  
A1EJD C3  C8  C 0 1 N N N N N N 44.819 -2.610 5.552  -3.010 4.083  0.413  C3  A1EJD 8  
A1EJD C9  C9  C 0 1 N N N N N N 44.700 -5.699 2.259  2.519  -0.009 0.008  C9  A1EJD 9  
A1EJD N29 N1  N 0 1 N N N N N N 42.948 -2.892 6.976  -1.831 3.598  -1.605 N29 A1EJD 10 
A1EJD N5  N2  N 0 1 N N N N N N 42.902 -3.838 4.854  -1.487 2.295  0.310  N5  A1EJD 11 
A1EJD O1  O1  O 0 1 N N N N N N 44.689 -1.692 7.749  -3.274 5.291  -1.510 O1  A1EJD 12 
A1EJD O10 O2  O 0 1 N N N N N N 44.955 -5.533 0.862  3.459  0.657  0.853  O10 A1EJD 13 
A1EJD O12 O3  O 0 1 N N N N N N 46.775 -4.083 1.703  5.733  1.764  1.571  O12 A1EJD 14 
A1EJD O13 O4  O 0 1 N N N N N N 45.127 -3.162 0.007  5.732  -0.567 0.355  O13 A1EJD 15 
A1EJD O14 O5  O 0 1 N N N N N N 46.794 -4.935 -0.679 5.085  1.550  -0.859 O14 A1EJD 16 
A1EJD O16 O6  O 0 1 N N N N N N 40.872 -6.089 1.638  0.133  -2.176 0.039  O16 A1EJD 17 
A1EJD O18 O7  O 0 1 N N N N N N 41.094 -8.177 0.238  0.417  -4.732 -0.506 O18 A1EJD 18 
A1EJD O19 O8  O 0 1 N N N N N N 38.831 -7.186 0.723  -1.001 -3.197 -2.102 O19 A1EJD 19 
A1EJD O20 O9  O 0 1 N N N N N N 40.420 -6.011 -0.845 1.506  -2.956 -1.931 O20 A1EJD 20 
A1EJD O22 O10 O 0 1 N N N N N N 40.830 -3.547 2.334  -1.852 -1.014 1.255  O22 A1EJD 21 
A1EJD O24 O11 O 0 1 N N N N N N 42.003 -1.304 2.074  -3.287 -2.653 -0.217 O24 A1EJD 22 
A1EJD O25 O12 O 0 1 N N N N N N 39.526 -1.514 2.558  -3.752 -2.454 2.363  O25 A1EJD 23 
A1EJD O26 O13 O 0 1 N N N N N N 40.442 -2.198 0.296  -4.289 -0.562 0.780  O26 A1EJD 24 
A1EJD O28 O14 O 0 1 N N N N N N 41.128 -4.058 6.284  -0.422 1.890  -1.589 O28 A1EJD 25 
A1EJD O7  O15 O 0 1 N N N N N N 42.938 -5.943 3.815  0.615  1.303  0.804  O7  A1EJD 26 
A1EJD P11 P1  P 0 1 N N N N N N 45.971 -4.343 0.446  5.004  0.866  0.451  P11 A1EJD 27 
A1EJD P17 P2  P 0 1 N N N N N N 40.280 -6.911 0.367  0.290  -3.259 -1.142 P17 A1EJD 28 
A1EJD P23 P3  P 0 1 N N N N N N 40.715 -2.029 1.774  -3.316 -1.647 1.039  P23 A1EJD 29 
A1EJD H1  H1  H 0 1 N N N N N N 44.622 -3.493 3.661  -2.587 2.822  2.052  H1  A1EJD 30 
A1EJD H2  H2  H 0 1 N N N N N N 41.213 -4.913 4.244  -1.062 1.154  2.024  H2  A1EJD 31 
A1EJD H3  H3  H 0 1 N N N N N N 43.259 -7.289 2.240  1.218  -0.505 1.669  H3  A1EJD 32 
A1EJD H4  H4  H 0 1 N N N N N N 42.543 -5.293 0.651  0.264  -0.546 -1.252 H4  A1EJD 33 
A1EJD H5  H5  H 0 1 N N N N N N 42.948 -3.525 2.197  -1.898 0.037  -0.539 H5  A1EJD 34 
A1EJD H6  H6  H 0 1 N N N N N N 45.811 -2.235 5.345  -3.720 4.686  0.958  H6  A1EJD 35 
A1EJD H7  H7  H 0 1 N N N N N N 45.415 -6.422 2.680  2.853  -1.031 -0.173 H7  A1EJD 36 
A1EJD H8  H8  H 0 1 N N N N N N 44.812 -4.732 2.771  2.443  0.522  -0.941 H8  A1EJD 37 
A1EJD H9  H9  H 0 1 N N N N N N 42.499 -2.738 7.856  -1.629 3.785  -2.536 H9  A1EJD 38 
A1EJD H10 H10 H 0 1 N N N N N N 47.678 -4.344 1.562  6.669  1.931  1.393  H10 A1EJD 39 
A1EJD H11 H11 H 0 1 N N N N N N 45.267 -2.999 -0.918 5.718  -1.071 1.179  H11 A1EJD 40 
A1EJD H12 H12 H 0 1 N N N N N N 41.552 -8.176 -0.594 0.514  -5.437 -1.161 H12 A1EJD 41 
A1EJD H13 H13 H 0 1 N N N N N N 38.263 -6.735 0.110  -1.835 -3.386 -1.651 H13 A1EJD 42 
A1EJD H14 H14 H 0 1 N N N N N N 42.433 -1.072 1.260  -2.669 -3.390 -0.116 H14 A1EJD 43 
A1EJD H15 H15 H 0 1 N N N N N N 38.792 -1.382 1.970  -4.626 -2.863 2.304  H15 A1EJD 44 
# 
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 
A1EJD O20 P17 DOUB N N 1  
A1EJD O14 P11 DOUB N N 2  
A1EJD O13 P11 SING N N 3  
A1EJD O18 P17 SING N N 4  
A1EJD O26 P23 DOUB N N 5  
A1EJD P17 O19 SING N N 6  
A1EJD P17 O16 SING N N 7  
A1EJD P11 O10 SING N N 8  
A1EJD P11 O12 SING N N 9  
A1EJD O10 C9  SING N N 10 
A1EJD O16 C15 SING N N 11 
A1EJD C15 C21 SING N N 12 
A1EJD C15 C8  SING N N 13 
A1EJD P23 O24 SING N N 14 
A1EJD P23 O22 SING N N 15 
A1EJD P23 O25 SING N N 16 
A1EJD C9  C8  SING N N 17 
A1EJD O22 C21 SING N N 18 
A1EJD C21 C6  SING N N 19 
A1EJD C8  O7  SING N N 20 
A1EJD O7  C6  SING N N 21 
A1EJD C6  N5  SING N N 22 
A1EJD C4  N5  SING N N 23 
A1EJD C4  C3  DOUB N N 24 
A1EJD N5  C27 SING N N 25 
A1EJD C3  C2  SING N N 26 
A1EJD C27 O28 DOUB N N 27 
A1EJD C27 N29 SING N N 28 
A1EJD C2  N29 SING N N 29 
A1EJD C2  O1  DOUB N N 30 
A1EJD C4  H1  SING N N 31 
A1EJD C6  H2  SING N N 32 
A1EJD C8  H3  SING N N 33 
A1EJD C15 H4  SING N N 34 
A1EJD C21 H5  SING N N 35 
A1EJD C3  H6  SING N N 36 
A1EJD C9  H7  SING N N 37 
A1EJD C9  H8  SING N N 38 
A1EJD N29 H9  SING N N 39 
A1EJD O12 H10 SING N N 40 
A1EJD O13 H11 SING N N 41 
A1EJD O18 H12 SING N N 42 
A1EJD O19 H13 SING N N 43 
A1EJD O24 H14 SING N N 44 
A1EJD O25 H15 SING N N 45 
# 
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 
A1EJD InChI            InChI                1.06  "InChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(13)10-5)8-7(26-29(20,21)22)6(25-28(17,18)19)4(24-8)3-23-27(14,15)16/h1-2,4,6-8H,3H2,(H,10,12,13)(H2,14,15,16)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,8-/m1/s1" 
A1EJD InChIKey         InChI                1.06  LGKMYXXYWOPMQI-XVFCMESISA-N                                                                                                                                                                       
A1EJD SMILES_CANONICAL CACTVS               3.385 "O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O[P](O)(O)=O)[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                
A1EJD SMILES           CACTVS               3.385 "O[P](O)(=O)OC[CH]1O[CH]([CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                     
A1EJD 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)OP(=O)(O)O)OP(=O)(O)O"                                                                                                                 
A1EJD SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O"                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1EJD 
_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]-3,4-diphosphonooxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1EJD 
_pdbx_chem_comp_synonyms.name         "3h-Uridine tri-phosphate" 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_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 
A1EJD "Create component" 2025-01-14 PDBC 
A1EJD "Initial release"  2025-11-12 RCSB 
# 
