data_A1EEG
# 
_chem_comp.id                                    A1EEG 
_chem_comp.name                                  "(6~{S},9~{a}~{S})-6-(2-methylpropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H34 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-10-20 
_chem_comp.pdbx_modified_date                    2025-02-14 
_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                        498.616 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EEG 
_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        9K2K 
_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 
A1EEG C10 C1  C 0 1 N N N N N N 146.076 12.882 7.365  -1.515 4.066  0.766  C10 A1EEG 1  
A1EEG C13 C2  C 0 1 N N S N N N 142.542 12.871 8.577  -0.602 0.604  -0.680 C13 A1EEG 2  
A1EEG C17 C3  C 0 1 Y N N N N N 142.212 12.999 12.783 3.274  -0.896 1.500  C17 A1EEG 3  
A1EEG C20 C4  C 0 1 Y N N N N N 145.498 14.487 13.042 3.269  -3.085 -1.463 C20 A1EEG 4  
A1EEG C21 C5  C 0 1 Y N N N N N 145.189 15.692 13.599 4.627  -3.107 -1.778 C21 A1EEG 5  
A1EEG C22 C6  C 0 1 Y N N N N N 143.883 16.009 13.892 5.531  -2.415 -1.032 C22 A1EEG 6  
A1EEG C24 C7  C 0 1 Y N N N N N 141.597 15.402 13.898 5.996  -0.941 0.868  C24 A1EEG 7  
A1EEG C26 C8  C 0 1 Y N N N N N 140.905 13.305 13.084 4.178  -0.205 2.246  C26 A1EEG 8  
A1EEG O01 O1  O 0 1 N N N N N N 142.231 15.424 7.376  -2.402 -0.984 -3.291 O01 A1EEG 9  
A1EEG C02 C9  C 0 1 N N N N N N 141.468 14.591 7.030  -2.093 -0.600 -2.179 C02 A1EEG 10 
A1EEG N03 N1  N 0 1 N N N N N N 141.535 13.271 7.606  -1.045 0.232  -2.021 N03 A1EEG 11 
A1EEG C04 C10 C 0 1 N N N N N N 140.705 12.185 7.212  -0.347 0.767  -3.196 C04 A1EEG 12 
A1EEG C05 C11 C 0 1 N N N N N N 141.540 11.290 6.386  -0.382 2.298  -3.106 C05 A1EEG 13 
A1EEG C06 C12 C 0 1 N N N N N N 142.887 10.945 7.022  0.101  2.718  -1.746 C06 A1EEG 14 
A1EEG N07 N2  N 0 1 N N N N N N 143.333 11.796 8.095  -0.030 1.952  -0.672 N07 A1EEG 15 
A1EEG C08 C13 C 0 1 N N S N N N 144.511 11.619 8.844  0.401  2.467  0.641  C08 A1EEG 16 
A1EEG C09 C14 C 0 1 N N N N N N 145.405 12.832 8.731  -0.824 2.887  1.455  C09 A1EEG 17 
A1EEG C11 C15 C 0 1 N N N N N N 146.769 14.213 7.143  -2.808 4.405  1.510  C11 A1EEG 18 
A1EEG C12 C16 C 0 1 N N N N N N 147.034 11.721 7.147  -0.584 5.280  0.779  C12 A1EEG 19 
A1EEG C14 C17 C 0 1 N N N N N N 141.934 12.435 9.884  0.470  -0.380 -0.204 C14 A1EEG 20 
A1EEG N15 N3  N 0 1 N N N N N N 142.847 11.858 10.740 1.128  0.118  0.997  N15 A1EEG 21 
A1EEG C16 C18 C 0 1 N N N N N N 142.539 11.663 12.155 1.810  -0.855 1.854  C16 A1EEG 22 
A1EEG C18 C19 C 0 1 Y N N N N N 143.208 13.896 13.061 3.712  -1.645 0.395  C18 A1EEG 23 
A1EEG C19 C20 C 0 1 Y N N N N N 144.506 13.584 12.763 2.809  -2.371 -0.400 C19 A1EEG 24 
A1EEG C23 C21 C 0 1 Y N N N N N 142.897 15.102 13.618 5.093  -1.667 0.074  C23 A1EEG 25 
A1EEG C25 C22 C 0 1 Y N N N N N 140.592 14.516 13.634 5.535  -0.226 1.931  C25 A1EEG 26 
A1EEG C27 C23 C 0 1 N N N N N N 144.108 11.456 10.285 1.141  1.379  1.370  C27 A1EEG 27 
A1EEG O28 O2  O 0 1 N N N N N N 144.881 10.951 11.024 1.778  1.675  2.358  O28 A1EEG 28 
A1EEG O29 O3  O 0 1 N N N N N N 143.596 10.047 6.677  0.638  3.800  -1.630 O29 A1EEG 29 
A1EEG N30 N4  N 0 1 N N N N N N 140.496 14.951 6.064  -2.799 -1.006 -1.106 N30 A1EEG 30 
A1EEG C31 C24 C 0 1 N N N N N N 140.485 16.294 5.516  -3.869 -1.995 -1.264 C31 A1EEG 31 
A1EEG C32 C25 C 0 1 Y N N N N N 139.379 17.134 6.072  -4.496 -2.275 0.078  C32 A1EEG 32 
A1EEG C33 C26 C 0 1 Y N N N N N 138.366 17.518 5.244  -3.992 -3.282 0.879  C33 A1EEG 33 
A1EEG C34 C27 C 0 1 Y N N N N N 137.335 18.274 5.722  -4.568 -3.539 2.109  C34 A1EEG 34 
A1EEG C35 C28 C 0 1 Y N N N N N 137.358 18.642 7.037  -5.646 -2.789 2.539  C35 A1EEG 35 
A1EEG C36 C29 C 0 1 Y N N N N N 138.391 18.257 7.856  -6.149 -1.781 1.737  C36 A1EEG 36 
A1EEG C37 C30 C 0 1 Y N N N N N 139.409 17.499 7.378  -5.571 -1.521 0.509  C37 A1EEG 37 
A1EEG H1  H1  H 0 1 N N N N N N 145.282 12.796 6.609  -1.748 3.798  -0.264 H1  A1EEG 38 
A1EEG H2  H2  H 0 1 N N N N N N 143.194 13.733 8.779  -1.451 0.569  0.003  H2  A1EEG 39 
A1EEG H3  H3  H 0 1 N N N N N N 146.527 14.244 12.820 2.573  -3.641 -2.072 H3  A1EEG 40 
A1EEG H4  H4  H 0 1 N N N N N N 145.974 16.402 13.812 4.966  -3.681 -2.628 H4  A1EEG 41 
A1EEG H5  H5  H 0 1 N N N N N N 143.639 16.964 14.334 6.580  -2.442 -1.288 H5  A1EEG 42 
A1EEG H6  H6  H 0 1 N N N N N N 141.357 16.359 14.337 7.051  -0.949 0.635  H6  A1EEG 43 
A1EEG H7  H7  H 0 1 N N N N N N 140.124 12.586 12.885 3.839  0.370  3.096  H7  A1EEG 44 
A1EEG H8  H8  H 0 1 N N N N N N 139.851 12.554 6.626  0.687  0.421  -3.201 H8  A1EEG 45 
A1EEG H9  H9  H 0 1 N N N N N N 140.337 11.648 8.099  -0.849 0.438  -4.106 H9  A1EEG 46 
A1EEG H10 H10 H 0 1 N N N N N N 141.728 11.783 5.421  0.263  2.729  -3.871 H10 A1EEG 47 
A1EEG H11 H11 H 0 1 N N N N N N 140.986 10.355 6.218  -1.406 2.643  -3.252 H11 A1EEG 48 
A1EEG H12 H12 H 0 1 N N N N N N 145.060 10.726 8.511  1.059  3.325  0.499  H12 A1EEG 49 
A1EEG H13 H13 H 0 1 N N N N N N 146.179 12.784 9.512  -0.511 3.184  2.456  H13 A1EEG 50 
A1EEG H14 H14 H 0 1 N N N N N N 144.800 13.740 8.869  -1.518 2.050  1.525  H14 A1EEG 51 
A1EEG H15 H15 H 0 1 N N N N N N 146.053 15.032 7.307  -2.574 4.673  2.541  H15 A1EEG 52 
A1EEG H16 H16 H 0 1 N N N N N N 147.607 14.312 7.848  -3.299 5.245  1.019  H16 A1EEG 53 
A1EEG H17 H17 H 0 1 N N N N N N 147.150 14.261 6.112  -3.470 3.540  1.501  H17 A1EEG 54 
A1EEG H18 H18 H 0 1 N N N N N N 146.504 10.772 7.315  0.337  5.038  0.249  H18 A1EEG 55 
A1EEG H19 H19 H 0 1 N N N N N N 147.417 11.750 6.116  -1.076 6.120  0.288  H19 A1EEG 56 
A1EEG H20 H20 H 0 1 N N N N N N 147.874 11.802 7.852  -0.351 5.548  1.810  H20 A1EEG 57 
A1EEG H21 H21 H 0 1 N N N N N N 141.499 13.316 10.379 0.005  -1.342 0.013  H21 A1EEG 58 
A1EEG H22 H22 H 0 1 N N N N N N 141.140 11.703 9.674  1.212  -0.511 -0.992 H22 A1EEG 59 
A1EEG H23 H23 H 0 1 N N N N N N 141.675 10.989 12.254 1.372  -1.841 1.704  H23 A1EEG 60 
A1EEG H24 H24 H 0 1 N N N N N N 143.409 11.221 12.663 1.696  -0.561 2.898  H24 A1EEG 61 
A1EEG H25 H25 H 0 1 N N N N N N 144.747 12.633 12.311 1.754  -2.363 -0.168 H25 A1EEG 62 
A1EEG H26 H26 H 0 1 N N N N N N 139.566 14.769 13.856 6.232  0.331  2.539  H26 A1EEG 63 
A1EEG H27 H27 H 0 1 N N N N N N 139.819 14.281 5.761  -2.599 -0.645 -0.228 H27 A1EEG 64 
A1EEG H28 H28 H 0 1 N N N N N N 141.445 16.777 5.749  -4.626 -1.605 -1.944 H28 A1EEG 65 
A1EEG H29 H29 H 0 1 N N N N N N 140.363 16.228 4.425  -3.454 -2.917 -1.671 H29 A1EEG 66 
A1EEG H30 H30 H 0 1 N N N N N N 138.379 17.223 4.205  -3.149 -3.869 0.544  H30 A1EEG 67 
A1EEG H31 H31 H 0 1 N N N N N N 136.522 18.573 5.077  -4.174 -4.327 2.735  H31 A1EEG 68 
A1EEG H32 H32 H 0 1 N N N N N N 136.555 19.243 7.437  -6.096 -2.991 3.500  H32 A1EEG 69 
A1EEG H33 H33 H 0 1 N N N N N N 138.393 18.561 8.892  -6.993 -1.195 2.072  H33 A1EEG 70 
A1EEG H34 H34 H 0 1 N N N N N N 140.222 17.194 8.020  -5.962 -0.731 -0.115 H34 A1EEG 71 
# 
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 
A1EEG C33 C34 DOUB Y N 1  
A1EEG C33 C32 SING Y N 2  
A1EEG C31 N30 SING N N 3  
A1EEG C31 C32 SING N N 4  
A1EEG C34 C35 SING Y N 5  
A1EEG N30 C02 SING N N 6  
A1EEG C32 C37 DOUB Y N 7  
A1EEG C05 C06 SING N N 8  
A1EEG C05 C04 SING N N 9  
A1EEG O29 C06 DOUB N N 10 
A1EEG C06 N07 SING N N 11 
A1EEG C02 O01 DOUB N N 12 
A1EEG C02 N03 SING N N 13 
A1EEG C35 C36 DOUB Y N 14 
A1EEG C11 C10 SING N N 15 
A1EEG C12 C10 SING N N 16 
A1EEG C04 N03 SING N N 17 
A1EEG C10 C09 SING N N 18 
A1EEG C37 C36 SING Y N 19 
A1EEG N03 C13 SING N N 20 
A1EEG N07 C13 SING N N 21 
A1EEG N07 C08 SING N N 22 
A1EEG C13 C14 SING N N 23 
A1EEG C09 C08 SING N N 24 
A1EEG C08 C27 SING N N 25 
A1EEG C14 N15 SING N N 26 
A1EEG C27 N15 SING N N 27 
A1EEG C27 O28 DOUB N N 28 
A1EEG N15 C16 SING N N 29 
A1EEG C16 C17 SING N N 30 
A1EEG C19 C20 DOUB Y N 31 
A1EEG C19 C18 SING Y N 32 
A1EEG C17 C18 DOUB Y N 33 
A1EEG C17 C26 SING Y N 34 
A1EEG C20 C21 SING Y N 35 
A1EEG C18 C23 SING Y N 36 
A1EEG C26 C25 DOUB Y N 37 
A1EEG C21 C22 DOUB Y N 38 
A1EEG C23 C22 SING Y N 39 
A1EEG C23 C24 DOUB Y N 40 
A1EEG C25 C24 SING Y N 41 
A1EEG C10 H1  SING N N 42 
A1EEG C13 H2  SING N N 43 
A1EEG C20 H3  SING N N 44 
A1EEG C21 H4  SING N N 45 
A1EEG C22 H5  SING N N 46 
A1EEG C24 H6  SING N N 47 
A1EEG C26 H7  SING N N 48 
A1EEG C04 H8  SING N N 49 
A1EEG C04 H9  SING N N 50 
A1EEG C05 H10 SING N N 51 
A1EEG C05 H11 SING N N 52 
A1EEG C08 H12 SING N N 53 
A1EEG C09 H13 SING N N 54 
A1EEG C09 H14 SING N N 55 
A1EEG C11 H15 SING N N 56 
A1EEG C11 H16 SING N N 57 
A1EEG C11 H17 SING N N 58 
A1EEG C12 H18 SING N N 59 
A1EEG C12 H19 SING N N 60 
A1EEG C12 H20 SING N N 61 
A1EEG C14 H21 SING N N 62 
A1EEG C14 H22 SING N N 63 
A1EEG C16 H23 SING N N 64 
A1EEG C16 H24 SING N N 65 
A1EEG C19 H25 SING N N 66 
A1EEG C25 H26 SING N N 67 
A1EEG N30 H27 SING N N 68 
A1EEG C31 H28 SING N N 69 
A1EEG C31 H29 SING N N 70 
A1EEG C33 H30 SING N N 71 
A1EEG C34 H31 SING N N 72 
A1EEG C35 H32 SING N N 73 
A1EEG C36 H33 SING N N 74 
A1EEG C37 H34 SING N N 75 
# 
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 
A1EEG InChI            InChI                1.06  "InChI=1S/C30H34N4O3/c1-21(2)17-26-29(36)32(19-24-13-8-12-23-11-6-7-14-25(23)24)20-27-33(16-15-28(35)34(26)27)30(37)31-18-22-9-4-3-5-10-22/h3-14,21,26-27H,15-20H2,1-2H3,(H,31,37)/t26-,27+/m0/s1" 
A1EEG InChIKey         InChI                1.06  HABVPTFNPWNZNJ-RRPNLBNLSA-N                                                                                                                                                                        
A1EEG SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@@H]1N2[C@H](CN(Cc3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCc5ccccc5"                                                                                                                            
A1EEG SMILES           CACTVS               3.385 "CC(C)C[CH]1N2[CH](CN(Cc3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCc5ccccc5"                                                                                                                               
A1EEG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@H]1C(=O)N(C[C@H]2N1C(=O)CCN2C(=O)NCc3ccccc3)Cc4cccc5c4cccc5"                                                                                                                             
A1EEG SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC1C(=O)N(CC2N1C(=O)CCN2C(=O)NCc3ccccc3)Cc4cccc5c4cccc5"                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           A1EEG 
_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        "(6~{S},9~{a}~{S})-6-(2-methylpropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1EEG "Create component" 2024-10-20 PDBC 
A1EEG "Initial release"  2025-02-19 RCSB 
# 
