data_A1JED
# 
_chem_comp.id                                    A1JED 
_chem_comp.name                                  "2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H15 N3 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-06-03 
_chem_comp.pdbx_modified_date                    2025-09-19 
_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                        285.298 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1JED 
_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        9RDI 
_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 
A1JED O1   O1  O 0 1 N N N N N N -15.147 16.490 -20.636 0.542  3.055  0.230  O1   A1JED 1  
A1JED O2   O2  O 0 1 N N N N N N -18.860 18.940 -22.939 -4.034 0.891  -0.458 O2   A1JED 2  
A1JED O3   O3  O 0 1 N N N N N N -16.469 18.336 -22.000 -2.238 2.710  0.136  O3   A1JED 3  
A1JED C14  C1  C 0 1 N N N N N N -19.030 17.729 -23.010 -3.210 0.056  -0.141 C14  A1JED 4  
A1JED C3   C2  C 0 1 N N N N N N -18.223 16.745 -22.357 -1.775 0.396  -0.077 C3   A1JED 5  
A1JED C2   C3  C 0 1 N N N N N N -17.012 17.103 -21.851 -1.354 1.685  0.057  C2   A1JED 6  
A1JED N3   N1  N 0 1 N N N N N N -20.043 17.232 -23.810 -3.587 -1.209 0.169  N3   A1JED 7  
A1JED C15  C4  C 0 1 N N N N N N -20.814 18.142 -24.648 -4.993 -1.612 0.083  C15  A1JED 8  
A1JED C13  C5  C 0 1 N N N N N N -20.347 15.811 -23.947 -2.557 -2.169 0.591  C13  A1JED 9  
A1JED C12  C6  C 0 1 N N N N N N -19.979 14.994 -22.733 -1.325 -1.998 -0.309 C12  A1JED 10 
A1JED N1   N2  N 0 1 N N N N N N -18.687 15.421 -22.150 -0.839 -0.615 -0.155 N1   A1JED 11 
A1JED C4   C7  C 0 1 N N N N N N -17.893 14.556 -21.392 0.470  -0.347 -0.095 C4   A1JED 12 
A1JED N2   N3  N 0 1 N N N N N N -16.747 14.903 -20.880 0.930  0.870  0.034  N2   A1JED 13 
A1JED C1   C8  C 0 1 N N N N N N -16.247 16.161 -21.088 0.101  1.923  0.113  C1   A1JED 14 
A1JED C5   C9  C 0 1 N N N N N N -18.330 13.109 -21.213 1.451  -1.489 -0.177 C5   A1JED 15 
A1JED C6   C10 C 0 1 Y N N N N N -17.555 12.191 -22.133 2.856  -0.951 -0.089 C6   A1JED 16 
A1JED C11  C11 C 0 1 Y N N N N N -16.322 11.686 -21.743 3.469  -0.818 1.143  C11  A1JED 17 
A1JED C10  C12 C 0 1 Y N N N N N -15.534 10.974 -22.634 4.758  -0.325 1.224  C10  A1JED 18 
A1JED C9   C13 C 0 1 Y N N N N N -15.972 10.750 -23.923 5.434  0.035  0.074  C9   A1JED 19 
A1JED C8   C14 C 0 1 Y N N N N N -17.195 11.242 -24.323 4.821  -0.098 -1.158 C8   A1JED 20 
A1JED C7   C15 C 0 1 Y N N N N N -17.984 11.955 -23.434 3.534  -0.597 -1.240 C7   A1JED 21 
A1JED HO3  H1  H 0 1 N N N N N N -17.117 18.926 -22.367 -1.826 3.579  0.229  HO3  A1JED 22 
A1JED H151 H2  H 0 0 N N N N N N -20.496 19.177 -24.455 -5.594 -0.764 -0.247 H151 A1JED 23 
A1JED H152 H3  H 0 0 N N N N N N -20.645 17.897 -25.707 -5.094 -2.429 -0.632 H152 A1JED 24 
A1JED H153 H4  H 0 0 N N N N N N -21.884 18.038 -24.414 -5.337 -1.942 1.063  H153 A1JED 25 
A1JED H131 H5  H 0 0 N N N N N N -21.427 15.702 -24.125 -2.282 -1.977 1.628  H131 A1JED 26 
A1JED H132 H6  H 0 0 N N N N N N -19.792 15.418 -24.812 -2.942 -3.184 0.495  H132 A1JED 27 
A1JED H122 H7  H 0 0 N N N N N N -20.767 15.110 -21.974 -0.546 -2.697 -0.004 H122 A1JED 28 
A1JED H121 H8  H 0 0 N N N N N N -19.905 13.936 -23.026 -1.599 -2.182 -1.347 H121 A1JED 29 
A1JED H51  H9  H 0 1 N N N N N N -19.403 13.026 -21.442 1.273  -2.180 0.646  H51  A1JED 30 
A1JED H52  H10 H 0 1 N N N N N N -18.153 12.806 -20.170 1.321  -2.012 -1.125 H52  A1JED 31 
A1JED H11  H11 H 0 1 N N N N N N -15.973 11.850 -20.734 2.940  -1.100 2.042  H11  A1JED 32 
A1JED H10  H12 H 0 1 N N N N N N -14.574 10.593 -22.318 5.236  -0.221 2.187  H10  A1JED 33 
A1JED H9   H13 H 0 1 N N N N N N -15.359 10.192 -24.615 6.440  0.421  0.138  H9   A1JED 34 
A1JED H8   H14 H 0 1 N N N N N N -17.540 11.072 -25.332 5.349  0.184  -2.057 H8   A1JED 35 
A1JED H7   H15 H 0 1 N N N N N N -18.944 12.332 -23.756 3.056  -0.701 -2.203 H7   A1JED 36 
# 
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 
A1JED C15 N3   SING N N 1  
A1JED C8  C9   DOUB Y N 2  
A1JED C8  C7   SING Y N 3  
A1JED C13 N3   SING N N 4  
A1JED C13 C12  SING N N 5  
A1JED C9  C10  SING Y N 6  
A1JED N3  C14  SING N N 7  
A1JED C7  C6   DOUB Y N 8  
A1JED C14 O2   DOUB N N 9  
A1JED C14 C3   SING N N 10 
A1JED C12 N1   SING N N 11 
A1JED C10 C11  DOUB Y N 12 
A1JED C3  N1   SING N N 13 
A1JED C3  C2   DOUB N N 14 
A1JED N1  C4   SING N N 15 
A1JED C6  C11  SING Y N 16 
A1JED C6  C5   SING N N 17 
A1JED O3  C2   SING N N 18 
A1JED C2  C1   SING N N 19 
A1JED C4  C5   SING N N 20 
A1JED C4  N2   DOUB N N 21 
A1JED C1  N2   SING N N 22 
A1JED C1  O1   DOUB N N 23 
A1JED O3  HO3  SING N N 24 
A1JED C15 H151 SING N N 25 
A1JED C15 H152 SING N N 26 
A1JED C15 H153 SING N N 27 
A1JED C13 H131 SING N N 28 
A1JED C13 H132 SING N N 29 
A1JED C12 H122 SING N N 30 
A1JED C12 H121 SING N N 31 
A1JED C5  H51  SING N N 32 
A1JED C5  H52  SING N N 33 
A1JED C11 H11  SING N N 34 
A1JED C10 H10  SING N N 35 
A1JED C9  H9   SING N N 36 
A1JED C8  H8   SING N N 37 
A1JED C7  H7   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 
A1JED InChI            InChI                1.06  "InChI=1S/C15H15N3O3/c1-17-7-8-18-11(9-10-5-3-2-4-6-10)16-14(20)13(19)12(18)15(17)21/h2-6,19H,7-9H2,1H3" 
A1JED InChIKey         InChI                1.06  RPOUCHBGKZYIOF-UHFFFAOYSA-N                                                                              
A1JED SMILES_CANONICAL CACTVS               3.385 "CN1CCN2C(=NC(=O)C(=C2C1=O)O)Cc3ccccc3"                                                                  
A1JED SMILES           CACTVS               3.385 "CN1CCN2C(=NC(=O)C(=C2C1=O)O)Cc3ccccc3"                                                                  
A1JED SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1CCN2C(=NC(=O)C(=C2C1=O)O)Cc3ccccc3"                                                                  
A1JED SMILES           "OpenEye OEToolkits" 2.0.7 "CN1CCN2C(=NC(=O)C(=C2C1=O)O)Cc3ccccc3"                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           A1JED 
_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-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1JED "Create component" 2025-06-03 PDBE 
A1JED "Initial release"  2025-09-24 RCSB 
# 
