data_A1EEL
# 
_chem_comp.id                                    A1EEL 
_chem_comp.name                                  "(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-~{N}-[(2~{S})-2-methylbutyl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-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                               "C28 H38 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-10-22 
_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                        478.626 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EEL 
_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        9K2B 
_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 
A1EEL C4  C1  C 0 1 N N N N N N 99.225  -10.860 -5.150  -5.074 0.826  -1.590 C4  A1EEL 1  
A1EEL C5  C2  C 0 1 N N N N N N 99.234  -11.208 -7.646  -4.154 2.231  0.260  C5  A1EEL 2  
A1EEL C7  C3  C 0 1 N N N N N N 99.014  -8.774  -7.945  -2.403 1.219  1.620  C7  A1EEL 3  
A1EEL C10 C4  C 0 1 N N N N N N 100.876 -7.562  -9.181  -0.831 0.104  3.116  C10 A1EEL 4  
A1EEL C15 C5  C 0 1 N N S N N N 98.890  -6.362  -8.497  -0.839 -0.356 0.624  C15 A1EEL 5  
A1EEL C20 C6  C 0 1 Y N N N N N 100.070 -3.533  -4.604  4.215  -0.422 -1.924 C20 A1EEL 6  
A1EEL C21 C7  C 0 1 Y N N N N N 99.762  -3.846  -3.291  5.540  -0.361 -1.496 C21 A1EEL 7  
A1EEL C22 C8  C 0 1 Y N N N N N 98.468  -3.836  -2.859  5.943  0.577  -0.595 C22 A1EEL 8  
A1EEL C24 C9  C 0 1 Y N N N N N 96.061  -3.473  -3.326  5.391  2.486  0.838  C24 A1EEL 9  
A1EEL C26 C10 C 0 1 Y N N N N N 95.360  -2.818  -5.517  3.143  3.318  0.859  C26 A1EEL 10 
A1EEL C28 C11 C 0 1 Y N N N N N 97.728  -3.183  -5.098  3.667  1.444  -0.532 C28 A1EEL 11 
A1EEL C1  C12 C 0 1 N N N N N N 100.032 -13.708 -4.994  -6.120 3.313  -2.866 C1  A1EEL 12 
A1EEL C2  C13 C 0 1 N N N N N N 100.500 -12.884 -6.173  -5.754 3.222  -1.384 C2  A1EEL 13 
A1EEL C3  C14 C 0 1 N N S N N N 100.007 -11.397 -6.351  -4.603 2.229  -1.203 C3  A1EEL 14 
A1EEL N6  N1  N 0 1 N N N N N N 99.627  -9.940  -8.232  -2.977 1.371  0.410  N6  A1EEL 15 
A1EEL O8  O1  O 0 1 N N N N N N 97.984  -8.712  -7.285  -2.802 1.868  2.568  O8  A1EEL 16 
A1EEL N9  N2  N 0 1 N N N N N N 99.585  -7.648  -8.489  -1.388 0.348  1.780  N9  A1EEL 17 
A1EEL C11 C15 C 0 1 N N N N N N 100.656 -7.339  -10.665 -0.935 -1.400 3.399  C11 A1EEL 18 
A1EEL C12 C16 C 0 1 N N N N N N 99.626  -6.263  -10.909 -0.347 -2.157 2.241  C12 A1EEL 19 
A1EEL O13 O2  O 0 1 N N N N N N 99.504  -5.800  -12.032 0.143  -3.246 2.451  O13 A1EEL 20 
A1EEL N14 N3  N 0 1 N N N N N N 98.880  -5.832  -9.868  -0.341 -1.683 0.991  N14 A1EEL 21 
A1EEL C16 C17 C 0 1 N N N N N N 99.495  -5.326  -7.567  0.321  0.451  0.036  C16 A1EEL 22 
A1EEL N17 N4  N 0 1 N N N N N N 99.032  -3.975  -7.900  1.054  -0.341 -0.942 N17 A1EEL 23 
A1EEL C18 C18 C 0 1 N N N N N N 99.469  -2.935  -6.958  1.860  0.375  -1.934 C18 A1EEL 24 
A1EEL C19 C19 C 0 1 Y N N N N N 99.094  -3.208  -5.517  3.287  0.458  -1.458 C19 A1EEL 25 
A1EEL C23 C20 C 0 1 Y N N N N N 97.415  -3.507  -3.745  5.012  1.499  -0.088 C23 A1EEL 26 
A1EEL C25 C21 C 0 1 Y N N N N N 95.064  -3.134  -4.202  4.465  3.372  1.295  C25 A1EEL 27 
A1EEL C27 C22 C 0 1 Y N N N N N 96.654  -2.838  -5.964  2.739  2.376  -0.037 C27 A1EEL 28 
A1EEL C29 C23 C 0 1 N N N N N N 98.297  -3.620  -8.998  1.043  -1.673 -0.997 C29 A1EEL 29 
A1EEL O30 O3  O 0 1 N N N N N N 97.920  -2.474  -9.198  1.755  -2.225 -1.809 O30 A1EEL 30 
A1EEL C31 C24 C 0 1 N N S N N N 97.969  -4.680  -10.034 0.189  -2.525 -0.098 C31 A1EEL 31 
A1EEL C32 C25 C 0 1 N N S N N N 96.462  -5.028  -10.105 -0.972 -3.113 -0.902 C32 A1EEL 32 
A1EEL C33 C26 C 0 1 N N N N N N 96.230  -6.394  -10.754 -0.426 -4.090 -1.946 C33 A1EEL 33 
A1EEL C34 C27 C 0 1 N N N N N N 95.767  -4.916  -8.720  -1.922 -3.854 0.042  C34 A1EEL 34 
A1EEL C35 C28 C 0 1 N N N N N N 94.490  -5.729  -8.585  -3.146 -4.335 -0.741 C35 A1EEL 35 
A1EEL H1  H1  H 0 1 N N N N N N 99.812  -11.012 -4.232  -5.910 0.535  -0.953 H1  A1EEL 36 
A1EEL H2  H2  H 0 1 N N N N N N 99.033  -9.786  -5.288  -5.394 0.825  -2.632 H2  A1EEL 37 
A1EEL H3  H3  H 0 1 N N N N N N 98.268  -11.396 -5.067  -4.255 0.119  -1.461 H3  A1EEL 38 
A1EEL H4  H4  H 0 1 N N N N N N 98.154  -11.202 -7.437  -3.902 3.247  0.562  H4  A1EEL 39 
A1EEL H5  H5  H 0 1 N N N N N N 99.468  -12.027 -8.342  -4.961 1.854  0.888  H5  A1EEL 40 
A1EEL H6  H6  H 0 1 N N N N N N 101.432 -8.499  -9.032  0.214  0.414  3.143  H6  A1EEL 41 
A1EEL H7  H7  H 0 1 N N N N N N 101.455 -6.723  -8.769  -1.400 0.661  3.860  H7  A1EEL 42 
A1EEL H8  H8  H 0 1 N N N N N N 97.849  -6.527  -8.182  -1.617 -0.470 -0.131 H8  A1EEL 43 
A1EEL H9  H9  H 0 1 N N N N N N 101.103 -3.544  -4.919  3.922  -1.176 -2.640 H9  A1EEL 44 
A1EEL H10 H10 H 0 1 N N N N N N 100.554 -4.101  -2.602  6.258  -1.068 -1.884 H10 A1EEL 45 
A1EEL H11 H11 H 0 1 N N N N N N 98.245  -4.081  -1.831  6.973  0.613  -0.272 H11 A1EEL 46 
A1EEL H12 H12 H 0 1 N N N N N N 95.813  -3.717  -2.304  6.413  2.540  1.185  H12 A1EEL 47 
A1EEL H13 H13 H 0 1 N N N N N N 94.563  -2.553  -6.196  2.428  4.033  1.238  H13 A1EEL 48 
A1EEL H14 H14 H 0 1 N N N N N N 100.482 -14.711 -5.045  -6.940 4.020  -2.995 H14 A1EEL 49 
A1EEL H15 H15 H 0 1 N N N N N N 100.338 -13.216 -4.059  -5.254 3.653  -3.434 H15 A1EEL 50 
A1EEL H16 H16 H 0 1 N N N N N N 98.936  -13.796 -5.021  -6.427 2.331  -3.226 H16 A1EEL 51 
A1EEL H17 H17 H 0 1 N N N N N N 100.196 -13.428 -7.079  -5.446 4.204  -1.024 H17 A1EEL 52 
A1EEL H18 H18 H 0 1 N N N N N N 101.598 -12.848 -6.118  -6.620 2.882  -0.816 H18 A1EEL 53 
A1EEL H19 H19 H 0 1 N N N N N N 100.916 -10.783 -6.433  -3.768 2.521  -1.839 H19 A1EEL 54 
A1EEL H20 H20 H 0 1 N N N N N N 100.389 -9.931  -8.880  -2.610 0.912  -0.362 H20 A1EEL 55 
A1EEL H21 H21 H 0 1 N N N N N N 100.309 -8.278  -11.121 -0.383 -1.638 4.309  H21 A1EEL 56 
A1EEL H22 H22 H 0 1 N N N N N N 101.607 -7.036  -11.127 -1.982 -1.676 3.525  H22 A1EEL 57 
A1EEL H23 H23 H 0 1 N N N N N N 99.203  -5.560  -6.532  -0.072 1.346  -0.448 H23 A1EEL 58 
A1EEL H24 H24 H 0 1 N N N N N N 100.591 -5.361  -7.656  0.997  0.745  0.839  H24 A1EEL 59 
A1EEL H25 H25 H 0 1 N N N N N N 100.564 -2.851  -7.020  1.824  -0.158 -2.885 H25 A1EEL 60 
A1EEL H26 H26 H 0 1 N N N N N N 99.011  -1.982  -7.259  1.462  1.382  -2.067 H26 A1EEL 61 
A1EEL H27 H27 H 0 1 N N N N N N 94.038  -3.113  -3.864  4.760  4.129  2.007  H27 A1EEL 62 
A1EEL H28 H28 H 0 1 N N N N N N 96.863  -2.587  -6.993  1.711  2.346  -0.366 H28 A1EEL 63 
A1EEL H29 H29 H 0 1 N N N N N N 98.213  -4.232  -11.009 0.791  -3.330 0.322  H29 A1EEL 64 
A1EEL H30 H30 H 0 1 N N N N N N 95.992  -4.277  -10.757 -1.511 -2.310 -1.403 H30 A1EEL 65 
A1EEL H31 H31 H 0 1 N N N N N N 95.151  -6.606  -10.787 0.041  -4.936 -1.442 H31 A1EEL 66 
A1EEL H32 H32 H 0 1 N N N N N N 96.634  -6.387  -11.777 -1.244 -4.447 -2.572 H32 A1EEL 67 
A1EEL H33 H33 H 0 1 N N N N N N 96.739  -7.171  -10.165 0.312  -3.583 -2.566 H33 A1EEL 68 
A1EEL H34 H34 H 0 1 N N N N N N 96.475  -5.260  -7.952  -1.408 -4.711 0.476  H34 A1EEL 69 
A1EEL H35 H35 H 0 1 N N N N N N 95.521  -3.858  -8.544  -2.242 -3.180 0.837  H35 A1EEL 70 
A1EEL H36 H36 H 0 1 N N N N N N 94.070  -5.589  -7.578  -3.660 -3.478 -1.175 H36 A1EEL 71 
A1EEL H37 H37 H 0 1 N N N N N N 93.760  -5.393  -9.336  -2.826 -5.008 -1.537 H37 A1EEL 72 
A1EEL H38 H38 H 0 1 N N N N N N 94.715  -6.794  -8.744  -3.823 -4.862 -0.069 H38 A1EEL 73 
# 
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 
A1EEL O13 C12 DOUB N N 1  
A1EEL C12 C11 SING N N 2  
A1EEL C12 N14 SING N N 3  
A1EEL C33 C32 SING N N 4  
A1EEL C11 C10 SING N N 5  
A1EEL C32 C31 SING N N 6  
A1EEL C32 C34 SING N N 7  
A1EEL C31 N14 SING N N 8  
A1EEL C31 C29 SING N N 9  
A1EEL N14 C15 SING N N 10 
A1EEL O30 C29 DOUB N N 11 
A1EEL C10 N9  SING N N 12 
A1EEL C29 N17 SING N N 13 
A1EEL C34 C35 SING N N 14 
A1EEL C15 N9  SING N N 15 
A1EEL C15 C16 SING N N 16 
A1EEL N9  C7  SING N N 17 
A1EEL N6  C7  SING N N 18 
A1EEL N6  C5  SING N N 19 
A1EEL C7  O8  DOUB N N 20 
A1EEL N17 C16 SING N N 21 
A1EEL N17 C18 SING N N 22 
A1EEL C5  C3  SING N N 23 
A1EEL C18 C19 SING N N 24 
A1EEL C3  C2  SING N N 25 
A1EEL C3  C4  SING N N 26 
A1EEL C2  C1  SING N N 27 
A1EEL C27 C26 DOUB Y N 28 
A1EEL C27 C28 SING Y N 29 
A1EEL C26 C25 SING Y N 30 
A1EEL C19 C28 DOUB Y N 31 
A1EEL C19 C20 SING Y N 32 
A1EEL C28 C23 SING Y N 33 
A1EEL C20 C21 DOUB Y N 34 
A1EEL C25 C24 DOUB Y N 35 
A1EEL C23 C24 SING Y N 36 
A1EEL C23 C22 DOUB Y N 37 
A1EEL C21 C22 SING Y N 38 
A1EEL C4  H1  SING N N 39 
A1EEL C4  H2  SING N N 40 
A1EEL C4  H3  SING N N 41 
A1EEL C5  H4  SING N N 42 
A1EEL C5  H5  SING N N 43 
A1EEL C10 H6  SING N N 44 
A1EEL C10 H7  SING N N 45 
A1EEL C15 H8  SING N N 46 
A1EEL C20 H9  SING N N 47 
A1EEL C21 H10 SING N N 48 
A1EEL C22 H11 SING N N 49 
A1EEL C24 H12 SING N N 50 
A1EEL C26 H13 SING N N 51 
A1EEL C1  H14 SING N N 52 
A1EEL C1  H15 SING N N 53 
A1EEL C1  H16 SING N N 54 
A1EEL C2  H17 SING N N 55 
A1EEL C2  H18 SING N N 56 
A1EEL C3  H19 SING N N 57 
A1EEL N6  H20 SING N N 58 
A1EEL C11 H21 SING N N 59 
A1EEL C11 H22 SING N N 60 
A1EEL C16 H23 SING N N 61 
A1EEL C16 H24 SING N N 62 
A1EEL C18 H25 SING N N 63 
A1EEL C18 H26 SING N N 64 
A1EEL C25 H27 SING N N 65 
A1EEL C27 H28 SING N N 66 
A1EEL C31 H29 SING N N 67 
A1EEL C32 H30 SING N N 68 
A1EEL C33 H31 SING N N 69 
A1EEL C33 H32 SING N N 70 
A1EEL C33 H33 SING N N 71 
A1EEL C34 H34 SING N N 72 
A1EEL C34 H35 SING N N 73 
A1EEL C35 H36 SING N N 74 
A1EEL C35 H37 SING N N 75 
A1EEL C35 H38 SING N N 76 
# 
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 
A1EEL InChI            InChI                1.06  "InChI=1S/C28H38N4O3/c1-5-19(3)16-29-28(35)31-15-14-25(33)32-24(31)18-30(27(34)26(32)20(4)6-2)17-22-12-9-11-21-10-7-8-13-23(21)22/h7-13,19-20,24,26H,5-6,14-18H2,1-4H3,(H,29,35)/t19-,20-,24+,26-/m0/s1" 
A1EEL InChIKey         InChI                1.06  DSUXNYPFVGTLTM-NLVWIRSPSA-N                                                                                                                                                                              
A1EEL SMILES_CANONICAL CACTVS               3.385 "CC[C@H](C)CNC(=O)N1CCC(=O)N2[C@@H]1CN(Cc3cccc4ccccc34)C(=O)[C@@H]2[C@@H](C)CC"                                                                                                                          
A1EEL SMILES           CACTVS               3.385 "CC[CH](C)CNC(=O)N1CCC(=O)N2[CH]1CN(Cc3cccc4ccccc34)C(=O)[CH]2[CH](C)CC"                                                                                                                                 
A1EEL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC[C@H](C)CNC(=O)N1CCC(=O)N2[C@@H]1CN(C(=O)[C@@H]2[C@@H](C)CC)Cc3cccc4c3cccc4"                                                                                                                          
A1EEL SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(C)CNC(=O)N1CCC(=O)N2C1CN(C(=O)C2C(C)CC)Cc3cccc4c3cccc4"                                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           A1EEL 
_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~{S})-butan-2-yl]-~{N}-[(2~{S})-2-methylbutyl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-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 
A1EEL "Create component" 2024-10-22 PDBC 
A1EEL "Initial release"  2025-02-19 RCSB 
# 
