data_5JR
# 
_chem_comp.id                                    5JR 
_chem_comp.name                                  "N-[2-[[3-(3,5-dimethoxyphenyl)-2-oxidanylidene-1-[3-(4-propanoylpiperazin-1-yl)propyl]-4H-pyrimido[4,5-d]pyrimidin-7-yl]amino]phenyl]propanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H42 N8 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-08-19 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        630.737 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5JR 
_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        7V29 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
5JR C1  C1  C 0 1 Y N N N N N 43.589 2.076  40.070 -4.911 1.211   -0.786 C1  5JR 1  
5JR N1  N1  N 0 1 N N N N N N 45.038 2.705  35.778 -1.008 0.840   1.018  N1  5JR 2  
5JR O1  O1  O 0 1 N N N N N N 42.287 1.468  41.930 -6.968 0.406   -1.665 O1  5JR 3  
5JR C2  C2  C 0 1 Y N N N N N 44.401 2.967  39.395 -4.209 2.169   -0.067 C2  5JR 4  
5JR N2  N2  N 0 1 N N N N N N 44.959 2.604  38.152 -2.826 2.040   0.106  N2  5JR 5  
5JR O2  O2  O 0 1 N N N N N N 44.670 5.666  41.816 -6.904 4.446   0.842  O2  5JR 6  
5JR C3  C3  C 0 1 Y N N N N N 44.773 4.154  40.009 -4.879 3.255   0.479  C3  5JR 7  
5JR N3  N3  N 0 1 Y N N N N N 47.582 -0.590 35.686 1.805  3.380   -0.499 N3  5JR 8  
5JR O3  O3  O 0 1 N N N N N N 43.515 3.885  36.943 -3.093 0.214   1.305  O3  5JR 9  
5JR C4  C4  C 0 1 Y N N N N N 44.294 4.462  41.272 -6.249 3.383   0.307  C4  5JR 10 
5JR N4  N4  N 0 1 Y N N N N N 46.191 1.033  34.590 1.248  1.491   0.725  N4  5JR 11 
5JR O4  O4  O 0 1 N N N N N N 50.946 0.997  31.085 8.167  1.595   -0.147 O4  5JR 12 
5JR C5  C5  C 0 1 Y N N N N N 43.454 3.585  41.938 -6.950 2.425   -0.410 C5  5JR 13 
5JR N5  N5  N 0 1 N N N N N N 47.363 -0.630 33.442 3.491  2.087   0.469  N5  5JR 14 
5JR O5  O5  O 0 1 N N N N N N 37.855 6.748  34.630 0.458  -8.602  0.191  O5  5JR 15 
5JR C6  C6  C 0 1 Y N N N N N 43.092 2.391  41.322 -6.281 1.340   -0.957 C6  5JR 16 
5JR N6  N6  N 0 1 N N N N N N 49.617 -0.651 31.863 5.998  1.204   -0.407 N6  5JR 17 
5JR C7  C7  C 0 1 N N N N N N 44.380 5.914  43.188 -8.315 4.514   0.626  C7  5JR 18 
5JR N7  N7  N 0 1 N N N N N N 41.662 3.760  32.953 0.333  -3.862  0.810  N7  5JR 19 
5JR C8  C8  C 0 1 N N N N N N 42.082 1.590  43.335 -8.377 0.601   -1.802 C8  5JR 20 
5JR N8  N8  N 0 1 N N N N N N 39.681 5.567  34.150 0.160  -6.443  -0.225 N8  5JR 21 
5JR C9  C9  C 0 1 Y N N N N N 46.427 1.094  36.939 -0.431 2.800   -0.251 C9  5JR 22 
5JR C10 C10 C 0 1 Y N N N N N 45.891 1.606  35.761 -0.046 1.694   0.509  C10 5JR 23 
5JR C11 C11 C 0 1 N N N N N N 44.443 3.096  36.964 -2.321 1.017   0.819  C11 5JR 24 
5JR C12 C12 C 0 1 N N N N N N 46.102 1.719  38.249 -1.904 3.022   -0.491 C12 5JR 25 
5JR C13 C13 C 0 1 Y N N N N N 47.309 -0.049 36.864 0.529  3.644   -0.754 C13 5JR 26 
5JR C14 C14 C 0 1 Y N N N N N 47.024 -0.027 34.602 2.148  2.326   0.227  C14 5JR 27 
5JR C15 C15 C 0 1 Y N N N N N 47.046 0.655  29.488 6.358  4.847   -0.780 C15 5JR 28 
5JR C16 C16 C 0 1 Y N N N N N 45.919 0.659  30.300 5.119  5.283   -0.346 C16 5JR 29 
5JR C17 C17 C 0 1 Y N N N N N 46.014 0.247  31.615 4.167  4.371   0.068  C17 5JR 30 
5JR C18 C18 C 0 1 Y N N N N N 47.236 -0.220 32.131 4.453  3.013   0.050  C18 5JR 31 
5JR C19 C19 C 0 1 Y N N N N N 48.383 -0.202 31.327 5.703  2.574   -0.387 C19 5JR 32 
5JR C20 C20 C 0 1 Y N N N N N 48.265 0.236  29.983 6.652  3.496   -0.801 C20 5JR 33 
5JR C21 C21 C 0 1 N N N N N N 50.817 -0.054 31.694 7.279  0.790   -0.334 C21 5JR 34 
5JR C22 C22 C 0 1 N N N N N N 51.984 -0.774 32.332 7.607  -0.673  -0.485 C22 5JR 35 
5JR C23 C23 C 0 1 N N N N N N 44.745 3.467  34.528 -0.571 -0.315  1.807  C23 5JR 36 
5JR C24 C24 C 0 1 N N N N N N 43.839 2.723  33.572 -0.343 -1.509  0.878  C24 5JR 37 
5JR C25 C25 C 0 1 N N N N N N 42.366 2.862  33.876 0.114  -2.715  1.702  C25 5JR 38 
5JR C26 C26 C 0 1 N N N N N N 51.951 -0.763 33.833 9.119  -0.871  -0.363 C26 5JR 39 
5JR C27 C27 C 0 1 N N N N N N 40.213 3.502  32.998 0.995  -4.963  1.523  C27 5JR 40 
5JR C28 C28 C 0 1 N N N N N N 39.583 4.111  34.227 1.368  -6.063  0.522  C28 5JR 41 
5JR C29 C29 C 0 1 N N N N N N 40.676 6.003  33.166 -0.635 -5.377  -0.853 C29 5JR 42 
5JR C30 C30 C 0 1 N N N N N N 41.933 5.168  33.291 -0.928 -4.304  0.201  C30 5JR 43 
5JR C31 C31 C 0 1 N N N N N N 38.973 6.367  34.975 -0.209 -7.735  -0.333 C31 5JR 44 
5JR C32 C32 C 0 1 N N N N N N 39.566 6.756  36.358 -1.451 -8.102  -1.104 C32 5JR 45 
5JR C33 C33 C 0 1 N N N N N N 40.645 7.823  36.240 -1.641 -9.620  -1.072 C33 5JR 46 
5JR H1  H1  H 0 1 N N N N N N 43.341 1.127  39.617 -4.390 0.368   -1.215 H1  5JR 47 
5JR H2  H2  H 0 1 N N N N N N 45.437 4.839  39.502 -4.333 4.001   1.039  H2  5JR 48 
5JR H3  H3  H 0 1 N N N N N N 43.084 3.825  42.924 -8.017 2.525   -0.544 H3  5JR 49 
5JR H4  H4  H 0 1 N N N N N N 47.779 -1.532 33.553 3.764  1.279   0.930  H4  5JR 50 
5JR H5  H5  H 0 1 N N N N N N 49.597 -1.484 32.416 5.281  0.554   -0.474 H5  5JR 51 
5JR H6  H6  H 0 1 N N N N N N 44.743 6.915  43.465 -8.714 5.409   1.105  H6  5JR 52 
5JR H7  H7  H 0 1 N N N N N N 43.293 5.862  43.348 -8.517 4.554   -0.444 H7  5JR 53 
5JR H8  H8  H 0 1 N N N N N N 44.879 5.157  43.811 -8.791 3.631   1.053  H8  5JR 54 
5JR H10 H10 H 0 1 N N N N N N 41.418 0.784  43.681 -8.839 0.619   -0.815 H10 5JR 55 
5JR H11 H11 H 0 1 N N N N N N 43.049 1.516  43.854 -8.565 1.549   -2.308 H11 5JR 56 
5JR H12 H12 H 0 1 N N N N N N 41.621 2.564  43.555 -8.802 -0.214  -2.388 H12 5JR 57 
5JR H13 H13 H 0 1 N N N N N N 45.877 0.925  38.977 -2.072 3.032   -1.568 H13 5JR 58 
5JR H14 H14 H 0 1 N N N N N N 46.972 2.297  38.594 -2.164 4.008   -0.104 H14 5JR 59 
5JR H15 H15 H 0 1 N N N N N N 47.743 -0.460 37.764 0.252  4.504   -1.346 H15 5JR 60 
5JR H16 H16 H 0 1 N N N N N N 46.968 0.982  28.462 7.097  5.564   -1.106 H16 5JR 61 
5JR H17 H17 H 0 1 N N N N N N 44.969 0.984  29.903 4.895  6.339   -0.331 H17 5JR 62 
5JR H18 H18 H 0 1 N N N N N N 45.143 0.284  32.252 3.201  4.714   0.406  H18 5JR 63 
5JR H19 H19 H 0 1 N N N N N N 49.135 0.242  29.343 7.620  3.160   -1.140 H19 5JR 64 
5JR H20 H20 H 0 1 N N N N N N 51.975 -1.820 31.992 7.102  -1.241  0.296  H20 5JR 65 
5JR H21 H21 H 0 1 N N N N N N 52.914 -0.289 32.001 7.273  -1.021  -1.462 H21 5JR 66 
5JR H22 H22 H 0 1 N N N N N N 45.696 3.677  34.016 0.359  -0.072  2.321  H22 5JR 67 
5JR H23 H23 H 0 1 N N N N N N 44.259 4.415  34.803 -1.337 -0.566  2.540  H23 5JR 68 
5JR H24 H24 H 0 1 N N N N N N 44.100 1.655  33.611 -1.272 -1.752  0.363  H24 5JR 69 
5JR H25 H25 H 0 1 N N N N N N 44.019 3.107  32.557 0.424  -1.259  0.145  H25 5JR 70 
5JR H26 H26 H 0 1 N N N N N N 42.257 3.256  34.897 -0.652 -2.966  2.435  H26 5JR 71 
5JR H27 H27 H 0 1 N N N N N N 41.902 1.866  33.815 1.044  -2.473  2.217  H27 5JR 72 
5JR H28 H28 H 0 1 N N N N N N 52.826 -1.303 34.223 9.357  -1.929  -0.472 H28 5JR 73 
5JR H29 H29 H 0 1 N N N N N N 51.971 0.276  34.192 9.625  -0.303  -1.143 H29 5JR 74 
5JR H30 H30 H 0 1 N N N N N N 51.031 -1.255 34.183 9.454  -0.523  0.615  H30 5JR 75 
5JR H31 H31 H 0 1 N N N N N N 39.744 3.937  32.103 1.898  -4.592  2.008  H31 5JR 76 
5JR H32 H32 H 0 1 N N N N N N 40.043 2.415  33.010 0.319  -5.370  2.274  H32 5JR 77 
5JR H33 H33 H 0 1 N N N N N N 38.525 3.816  34.281 1.755  -6.930  1.058  H33 5JR 78 
5JR H34 H34 H 0 1 N N N N N N 40.109 3.754  35.125 2.124  -5.689  -0.168 H34 5JR 79 
5JR H35 H35 H 0 1 N N N N N N 40.923 7.060  33.342 -0.071 -4.937  -1.676 H35 5JR 80 
5JR H36 H36 H 0 1 N N N N N N 40.261 5.887  32.154 -1.572 -5.789  -1.227 H36 5JR 81 
5JR H37 H37 H 0 1 N N N N N N 42.303 5.226  34.325 -1.578 -4.719  0.971  H37 5JR 82 
5JR H38 H38 H 0 1 N N N N N N 42.698 5.563  32.606 -1.421 -3.454  -0.272 H38 5JR 83 
5JR H39 H39 H 0 1 N N N N N N 38.756 7.140  36.996 -2.316 -7.618  -0.651 H39 5JR 84 
5JR H40 H40 H 0 1 N N N N N N 40.003 5.859  36.821 -1.348 -7.771  -2.137 H40 5JR 85 
5JR H41 H41 H 0 1 N N N N N N 41.033 8.065  37.240 -0.775 -10.104 -1.525 H41 5JR 86 
5JR H42 H42 H 0 1 N N N N N N 41.465 7.447  35.610 -1.743 -9.952  -0.039 H42 5JR 87 
5JR H43 H43 H 0 1 N N N N N N 40.217 8.728  35.784 -2.539 -9.886  -1.630 H43 5JR 88 
# 
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 
5JR C15 C20 DOUB Y N 1  
5JR C15 C16 SING Y N 2  
5JR C20 C19 SING Y N 3  
5JR C16 C17 DOUB Y N 4  
5JR O4  C21 DOUB N N 5  
5JR C19 N6  SING N N 6  
5JR C19 C18 DOUB Y N 7  
5JR C17 C18 SING Y N 8  
5JR C21 N6  SING N N 9  
5JR C21 C22 SING N N 10 
5JR C18 N5  SING N N 11 
5JR C22 C26 SING N N 12 
5JR N7  C27 SING N N 13 
5JR N7  C30 SING N N 14 
5JR N7  C25 SING N N 15 
5JR C27 C28 SING N N 16 
5JR C29 C30 SING N N 17 
5JR C29 N8  SING N N 18 
5JR N5  C14 SING N N 19 
5JR C24 C25 SING N N 20 
5JR C24 C23 SING N N 21 
5JR N8  C28 SING N N 22 
5JR N8  C31 SING N N 23 
5JR C23 N1  SING N N 24 
5JR N4  C14 DOUB Y N 25 
5JR N4  C10 SING Y N 26 
5JR C14 N3  SING Y N 27 
5JR O5  C31 DOUB N N 28 
5JR C31 C32 SING N N 29 
5JR N3  C13 DOUB Y N 30 
5JR C10 N1  SING N N 31 
5JR C10 C9  DOUB Y N 32 
5JR N1  C11 SING N N 33 
5JR C33 C32 SING N N 34 
5JR C13 C9  SING Y N 35 
5JR C9  C12 SING N N 36 
5JR O3  C11 DOUB N N 37 
5JR C11 N2  SING N N 38 
5JR N2  C12 SING N N 39 
5JR N2  C2  SING N N 40 
5JR C2  C3  DOUB Y N 41 
5JR C2  C1  SING Y N 42 
5JR C3  C4  SING Y N 43 
5JR C1  C6  DOUB Y N 44 
5JR C4  O2  SING N N 45 
5JR C4  C5  DOUB Y N 46 
5JR C6  O1  SING N N 47 
5JR C6  C5  SING Y N 48 
5JR O2  C7  SING N N 49 
5JR O1  C8  SING N N 50 
5JR C1  H1  SING N N 51 
5JR C3  H2  SING N N 52 
5JR C5  H3  SING N N 53 
5JR N5  H4  SING N N 54 
5JR N6  H5  SING N N 55 
5JR C7  H6  SING N N 56 
5JR C7  H7  SING N N 57 
5JR C7  H8  SING N N 58 
5JR C8  H10 SING N N 59 
5JR C8  H11 SING N N 60 
5JR C8  H12 SING N N 61 
5JR C12 H13 SING N N 62 
5JR C12 H14 SING N N 63 
5JR C13 H15 SING N N 64 
5JR C15 H16 SING N N 65 
5JR C16 H17 SING N N 66 
5JR C17 H18 SING N N 67 
5JR C20 H19 SING N N 68 
5JR C22 H20 SING N N 69 
5JR C22 H21 SING N N 70 
5JR C23 H22 SING N N 71 
5JR C23 H23 SING N N 72 
5JR C24 H24 SING N N 73 
5JR C24 H25 SING N N 74 
5JR C25 H26 SING N N 75 
5JR C25 H27 SING N N 76 
5JR C26 H28 SING N N 77 
5JR C26 H29 SING N N 78 
5JR C26 H30 SING N N 79 
5JR C27 H31 SING N N 80 
5JR C27 H32 SING N N 81 
5JR C28 H33 SING N N 82 
5JR C28 H34 SING N N 83 
5JR C29 H35 SING N N 84 
5JR C29 H36 SING N N 85 
5JR C30 H37 SING N N 86 
5JR C30 H38 SING N N 87 
5JR C32 H39 SING N N 88 
5JR C32 H40 SING N N 89 
5JR C33 H41 SING N N 90 
5JR C33 H42 SING N N 91 
5JR C33 H43 SING N N 92 
# 
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 
5JR InChI            InChI                1.03  "InChI=1S/C33H42N8O5/c1-5-29(42)35-27-10-7-8-11-28(27)36-32-34-21-23-22-41(24-18-25(45-3)20-26(19-24)46-4)33(44)40(31(23)37-32)13-9-12-38-14-16-39(17-15-38)30(43)6-2/h7-8,10-11,18-21H,5-6,9,12-17,22H2,1-4H3,(H,35,42)(H,34,36,37)" 
5JR InChIKey         InChI                1.03  YKUVMKFEISXAJC-UHFFFAOYSA-N                                                                                                                                                                                                           
5JR SMILES_CANONICAL CACTVS               3.385 "CCC(=O)Nc1ccccc1Nc2ncc3CN(C(=O)N(CCCN4CCN(CC4)C(=O)CC)c3n2)c5cc(OC)cc(OC)c5"                                                                                                                                                         
5JR SMILES           CACTVS               3.385 "CCC(=O)Nc1ccccc1Nc2ncc3CN(C(=O)N(CCCN4CCN(CC4)C(=O)CC)c3n2)c5cc(OC)cc(OC)c5"                                                                                                                                                         
5JR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1ccccc1Nc2ncc3c(n2)N(C(=O)N(C3)c4cc(cc(c4)OC)OC)CCCN5CCN(CC5)C(=O)CC"                                                                                                                                                       
5JR SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1ccccc1Nc2ncc3c(n2)N(C(=O)N(C3)c4cc(cc(c4)OC)OC)CCCN5CCN(CC5)C(=O)CC"                                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           5JR 
_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        "~{N}-[2-[[3-(3,5-dimethoxyphenyl)-2-oxidanylidene-1-[3-(4-propanoylpiperazin-1-yl)propyl]-4~{H}-pyrimido[4,5-d]pyrimidin-7-yl]amino]phenyl]propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
5JR "Create component" 2021-08-19 PDBJ 
5JR "Initial release"  2022-03-30 RCSB 
5JR "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            5JR 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C26 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
