data_A1EEF
# 
_chem_comp.id                                    A1EEF 
_chem_comp.name                                  "(6~{S},9~{a}~{S})-6-(1~{H}-imidazol-5-ylmethyl)-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 H30 N6 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                        522.598 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EEF 
_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        9K2C 
_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 
A1EEF C10 C1  C 0 1 Y N N N N N 100.514 43.347 28.846 -1.945 3.478  1.003  C10 A1EEF 1  
A1EEF C17 C2  C 0 1 N N S N N N 99.365  40.540 26.569 -0.528 0.270  -0.613 C17 A1EEF 2  
A1EEF C20 C3  C 0 1 N N N N N N 100.064 37.274 28.509 2.135  -0.885 1.824  C20 A1EEF 3  
A1EEF C21 C4  C 0 1 Y N N N N N 98.644  36.893 28.954 3.579  -0.664 1.456  C21 A1EEF 4  
A1EEF C22 C5  C 0 1 Y N N N N N 98.012  37.468 30.065 4.121  -1.283 0.317  C22 A1EEF 5  
A1EEF C24 C6  C 0 1 Y N N N N N 97.991  38.997 31.966 3.898  -2.697 -1.599 C24 A1EEF 6  
A1EEF C26 C7  C 0 1 Y N N N N N 96.054  37.637 31.534 6.023  -1.681 -1.153 C26 A1EEF 7  
A1EEF C28 C8  C 0 1 Y N N N N N 96.057  36.104 29.638 6.263  -0.230 0.806  C28 A1EEF 8  
A1EEF O01 O1  O 0 1 N N N N N N 96.876  41.795 25.925 -2.108 -1.483 -3.261 O01 A1EEF 9  
A1EEF C02 C9  C 0 1 N N N N N N 97.572  41.535 24.955 -1.836 -1.102 -2.139 C02 A1EEF 10 
A1EEF N03 N1  N 0 1 N N N N N N 98.862  40.824 25.184 -0.934 -0.116 -1.962 N03 A1EEF 11 
A1EEF C04 C10 C 0 1 N N N N N N 99.819  40.507 24.133 -0.359 0.572  -3.124 C04 A1EEF 12 
A1EEF C05 C11 C 0 1 N N N N N N 100.880 41.544 24.220 -0.642 2.071  -2.968 C05 A1EEF 13 
A1EEF C06 C12 C 0 1 N N N N N N 101.531 41.566 25.614 -0.204 2.511  -1.599 C06 A1EEF 14 
A1EEF N07 N2  N 0 1 N N N N N N 100.721 41.055 26.764 -0.189 1.692  -0.543 N07 A1EEF 15 
A1EEF C08 C13 C 0 1 N N S N N N 101.150 40.973 28.068 0.184  2.227  0.781  C08 A1EEF 16 
A1EEF C09 C14 C 0 1 N N N N N N 100.344 41.840 29.066 -1.075 2.419  1.629  C09 A1EEF 17 
A1EEF N11 N3  N 0 1 Y N N N N N 100.823 43.910 27.640 -1.964 4.810  1.318  N11 A1EEF 18 
A1EEF C12 C15 C 0 1 Y N N N N N 100.897 45.216 27.802 -2.884 5.397  0.522  C12 A1EEF 19 
A1EEF N13 N4  N 0 1 Y N N N N N 100.644 45.497 29.072 -3.412 4.485  -0.248 N13 A1EEF 20 
A1EEF C14 C16 C 0 1 Y N N N N N 100.410 44.367 29.728 -2.850 3.298  0.022  C14 A1EEF 21 
A1EEF C18 C17 C 0 1 N N N N N N 99.291  39.053 26.920 0.701  -0.543 -0.197 C18 A1EEF 22 
A1EEF N19 N5  N 0 1 N N N N N N 100.123 38.643 27.985 1.286  -0.000 1.022  N19 A1EEF 23 
A1EEF C23 C18 C 0 1 Y N N N N N 98.636  38.439 30.860 3.339  -2.115 -0.502 C23 A1EEF 24 
A1EEF C25 C19 C 0 1 Y N N N N N 96.702  38.597 32.309 5.236  -2.481 -1.923 C25 A1EEF 25 
A1EEF C27 C20 C 0 1 Y N N N N N 96.717  37.064 30.399 5.482  -1.062 -0.013 C27 A1EEF 26 
A1EEF C29 C21 C 0 1 Y N N N N N 96.686  35.537 28.537 5.703  0.357  1.899  C29 A1EEF 27 
A1EEF C30 C22 C 0 1 Y N N N N N 97.975  35.927 28.200 4.365  0.141  2.223  C30 A1EEF 28 
A1EEF C31 C23 C 0 1 N N N N N N 101.096 39.597 28.576 1.103  1.247  1.457  C31 A1EEF 29 
A1EEF O32 O2  O 0 1 N N N N N N 101.833 39.259 29.489 1.705  1.608  2.446  O32 A1EEF 30 
A1EEF O33 O3  O 0 1 N N N N N N 102.663 41.988 25.760 0.151  3.661  -1.446 O33 A1EEF 31 
A1EEF N34 N6  N 0 1 N N N N N N 97.127  41.867 23.602 -2.437 -1.666 -1.072 N34 A1EEF 32 
A1EEF C35 C24 C 0 1 N N N N N N 95.842  42.552 23.353 -3.496 -2.659 -1.268 C35 A1EEF 33 
A1EEF C36 C25 C 0 1 Y N N N N N 94.642  41.609 23.095 -3.997 -3.130 0.073  C36 A1EEF 34 
A1EEF C37 C26 C 0 1 Y N N N N N 93.833  41.816 21.976 -3.405 -4.216 0.690  C37 A1EEF 35 
A1EEF C38 C27 C 0 1 Y N N N N N 92.742  40.989 21.747 -3.865 -4.648 1.920  C38 A1EEF 36 
A1EEF C39 C28 C 0 1 Y N N N N N 92.455  39.956 22.630 -4.917 -3.994 2.533  C39 A1EEF 37 
A1EEF C41 C29 C 0 1 Y N N N N N 93.261  39.758 23.751 -5.509 -2.907 1.917  C41 A1EEF 38 
A1EEF C42 C30 C 0 1 Y N N N N N 94.350  40.587 23.986 -5.045 -2.472 0.689  C42 A1EEF 39 
A1EEF H1  H1  H 0 1 N N N N N N 98.703  41.068 27.271 -1.348 0.060  0.074  H1  A1EEF 40 
A1EEF H2  H2  H 0 1 N N N N N N 100.389 36.577 27.722 1.865  -1.923 1.629  H2  A1EEF 41 
A1EEF H3  H3  H 0 1 N N N N N N 100.741 37.194 29.372 1.991  -0.665 2.882  H3  A1EEF 42 
A1EEF H4  H4  H 0 1 N N N N N N 98.496  39.745 32.560 3.295  -3.337 -2.226 H4  A1EEF 43 
A1EEF H5  H5  H 0 1 N N N N N N 95.052  37.324 31.788 7.058  -1.523 -1.416 H5  A1EEF 44 
A1EEF H6  H6  H 0 1 N N N N N N 95.055  35.800 29.904 7.301  -0.053 0.567  H6  A1EEF 45 
A1EEF H7  H7  H 0 1 N N N N N N 99.331  40.541 23.148 0.717  0.401  -3.159 H7  A1EEF 46 
A1EEF H8  H8  H 0 1 N N N N N N 100.248 39.507 24.295 -0.823 0.202  -4.039 H8  A1EEF 47 
A1EEF H9  H9  H 0 1 N N N N N N 101.653 41.329 23.467 -0.089 2.627  -3.725 H9  A1EEF 48 
A1EEF H10 H10 H 0 1 N N N N N N 100.435 42.529 24.017 -1.710 2.255  -3.086 H10 A1EEF 49 
A1EEF H11 H11 H 0 1 N N N N N N 102.195 41.311 28.124 0.694  3.182  0.659  H11 A1EEF 50 
A1EEF H12 H12 H 0 1 N N N N N N 99.278  41.591 28.960 -0.792 2.729  2.635  H12 A1EEF 51 
A1EEF H13 H13 H 0 1 N N N N N N 100.678 41.598 30.086 -1.626 1.480  1.680  H13 A1EEF 52 
A1EEF H14 H14 H 0 1 N N N N N N 100.968 43.416 26.782 -1.418 5.251  1.988  H14 A1EEF 53 
A1EEF H15 H15 H 0 1 N N N N N N 101.125 45.936 27.030 -3.139 6.446  0.523  H15 A1EEF 54 
A1EEF H17 H17 H 0 1 N N N N N N 100.178 44.278 30.779 -3.085 2.360  -0.460 H17 A1EEF 55 
A1EEF H18 H18 H 0 1 N N N N N N 98.251  38.819 27.192 0.406  -1.578 -0.024 H18 A1EEF 56 
A1EEF H19 H19 H 0 1 N N N N N N 99.575  38.478 26.026 1.441  -0.510 -0.996 H19 A1EEF 57 
A1EEF H20 H20 H 0 1 N N N N N N 99.636  38.762 30.612 2.301  -2.292 -0.264 H20 A1EEF 58 
A1EEF H21 H21 H 0 1 N N N N N N 96.209  39.027 33.168 5.655  -2.955 -2.798 H21 A1EEF 59 
A1EEF H22 H22 H 0 1 N N N N N N 96.173  34.794 27.944 6.306  0.996  2.527  H22 A1EEF 60 
A1EEF H23 H23 H 0 1 N N N N N N 98.464  35.479 27.348 3.945  0.618  3.096  H23 A1EEF 61 
A1EEF H24 H24 H 0 1 N N N N N N 97.708  41.624 22.825 -2.167 -1.415 -0.175 H24 A1EEF 62 
A1EEF H25 H25 H 0 1 N N N N N N 95.964  43.199 22.472 -4.318 -2.208 -1.825 H25 A1EEF 63 
A1EEF H26 H26 H 0 1 N N N N N N 95.608  43.170 24.232 -3.101 -3.507 -1.826 H26 A1EEF 64 
A1EEF H27 H27 H 0 1 N N N N N N 94.056  42.619 21.289 -2.583 -4.727 0.211  H27 A1EEF 65 
A1EEF H28 H28 H 0 1 N N N N N N 92.116  41.149 20.882 -3.402 -5.497 2.401  H28 A1EEF 66 
A1EEF H29 H29 H 0 1 N N N N N N 91.610  39.308 22.449 -5.276 -4.332 3.494  H29 A1EEF 67 
A1EEF H30 H30 H 0 1 N N N N N N 93.037  38.956 24.439 -6.331 -2.396 2.396  H30 A1EEF 68 
A1EEF H31 H31 H 0 1 N N N N N N 94.967  40.436 24.859 -5.505 -1.621 0.209  H31 A1EEF 69 
# 
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 
A1EEF C38 C37 DOUB Y N 1  
A1EEF C38 C39 SING Y N 2  
A1EEF C37 C36 SING Y N 3  
A1EEF C39 C41 DOUB Y N 4  
A1EEF C36 C35 SING N N 5  
A1EEF C36 C42 DOUB Y N 6  
A1EEF C35 N34 SING N N 7  
A1EEF N34 C02 SING N N 8  
A1EEF C41 C42 SING Y N 9  
A1EEF C04 C05 SING N N 10 
A1EEF C04 N03 SING N N 11 
A1EEF C05 C06 SING N N 12 
A1EEF C02 N03 SING N N 13 
A1EEF C02 O01 DOUB N N 14 
A1EEF N03 C17 SING N N 15 
A1EEF C06 O33 DOUB N N 16 
A1EEF C06 N07 SING N N 17 
A1EEF C17 N07 SING N N 18 
A1EEF C17 C18 SING N N 19 
A1EEF N07 C08 SING N N 20 
A1EEF C18 N19 SING N N 21 
A1EEF N11 C12 SING Y N 22 
A1EEF N11 C10 SING Y N 23 
A1EEF C12 N13 DOUB Y N 24 
A1EEF N19 C20 SING N N 25 
A1EEF N19 C31 SING N N 26 
A1EEF C08 C31 SING N N 27 
A1EEF C08 C09 SING N N 28 
A1EEF C30 C29 DOUB Y N 29 
A1EEF C30 C21 SING Y N 30 
A1EEF C20 C21 SING N N 31 
A1EEF C29 C28 SING Y N 32 
A1EEF C31 O32 DOUB N N 33 
A1EEF C10 C09 SING N N 34 
A1EEF C10 C14 DOUB Y N 35 
A1EEF C21 C22 DOUB Y N 36 
A1EEF N13 C14 SING Y N 37 
A1EEF C28 C27 DOUB Y N 38 
A1EEF C22 C27 SING Y N 39 
A1EEF C22 C23 SING Y N 40 
A1EEF C27 C26 SING Y N 41 
A1EEF C23 C24 DOUB Y N 42 
A1EEF C26 C25 DOUB Y N 43 
A1EEF C24 C25 SING Y N 44 
A1EEF C17 H1  SING N N 45 
A1EEF C20 H2  SING N N 46 
A1EEF C20 H3  SING N N 47 
A1EEF C24 H4  SING N N 48 
A1EEF C26 H5  SING N N 49 
A1EEF C28 H6  SING N N 50 
A1EEF C04 H7  SING N N 51 
A1EEF C04 H8  SING N N 52 
A1EEF C05 H9  SING N N 53 
A1EEF C05 H10 SING N N 54 
A1EEF C08 H11 SING N N 55 
A1EEF C09 H12 SING N N 56 
A1EEF C09 H13 SING N N 57 
A1EEF N11 H14 SING N N 58 
A1EEF C12 H15 SING N N 59 
A1EEF C14 H17 SING N N 60 
A1EEF C18 H18 SING N N 61 
A1EEF C18 H19 SING N N 62 
A1EEF C23 H20 SING N N 63 
A1EEF C25 H21 SING N N 64 
A1EEF C29 H22 SING N N 65 
A1EEF C30 H23 SING N N 66 
A1EEF N34 H24 SING N N 67 
A1EEF C35 H25 SING N N 68 
A1EEF C35 H26 SING N N 69 
A1EEF C37 H27 SING N N 70 
A1EEF C38 H28 SING N N 71 
A1EEF C39 H29 SING N N 72 
A1EEF C41 H30 SING N N 73 
A1EEF C42 H31 SING N N 74 
# 
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 
A1EEF InChI            InChI                1.06  "InChI=1S/C30H30N6O3/c37-28-13-14-35(30(39)32-16-21-7-2-1-3-8-21)27-19-34(18-23-11-6-10-22-9-4-5-12-25(22)23)29(38)26(36(27)28)15-24-17-31-20-33-24/h1-12,17,20,26-27H,13-16,18-19H2,(H,31,33)(H,32,39)/t26-,27+/m0/s1" 
A1EEF InChIKey         InChI                1.06  ZXICHRIOFQGVQP-RRPNLBNLSA-N                                                                                                                                                                                             
A1EEF SMILES_CANONICAL CACTVS               3.385 "O=C1CCN([C@H]2CN(Cc3cccc4ccccc34)C(=O)[C@H](Cc5[nH]cnc5)N12)C(=O)NCc6ccccc6"                                                                                                                                           
A1EEF SMILES           CACTVS               3.385 "O=C1CCN([CH]2CN(Cc3cccc4ccccc34)C(=O)[CH](Cc5[nH]cnc5)N12)C(=O)NCc6ccccc6"                                                                                                                                             
A1EEF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)N2CCC(=O)N3[C@@H]2CN(C(=O)[C@@H]3Cc4cnc[nH]4)Cc5cccc6c5cccc6"                                                                                                                                         
A1EEF SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)N2CCC(=O)N3C2CN(C(=O)C3Cc4cnc[nH]4)Cc5cccc6c5cccc6"                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1EEF 
_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-(1~{H}-imidazol-5-ylmethyl)-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 
A1EEF "Create component" 2024-10-20 PDBC 
A1EEF "Initial release"  2025-02-19 RCSB 
# 
