data_K9M
# 
_chem_comp.id                                    K9M 
_chem_comp.name                                  "1-{4-[7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H27 N5 O" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-11-14 
_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                        401.504 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     K9M 
_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        6N2J 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
K9M C18 C1  C 0 1 Y N N N N N 18.872 3.873  -25.510 -4.356 1.093  -1.518 C18 K9M 1  
K9M N5  N1  N 0 1 Y N N N N N 25.100 4.723  -22.117 1.837  2.091  1.393  N5  K9M 2  
K9M C13 C2  C 0 1 N N N N N N 27.118 0.935  -22.679 4.408  0.189  -1.556 C13 K9M 3  
K9M C12 C3  C 0 1 N N N N N N 26.683 2.393  -22.521 3.450  1.127  -0.815 C12 K9M 4  
K9M C17 C4  C 0 1 Y N N N N N 19.108 3.824  -24.121 -3.846 0.246  -0.556 C17 K9M 5  
K9M C16 C5  C 0 1 N N N N N N 24.558 1.244  -21.688 3.191  -0.449 1.009  C16 K9M 6  
K9M C15 C6  C 0 1 N N N N N N 25.449 0.478  -20.759 4.139  -1.452 0.343  C15 K9M 7  
K9M N3  N2  N 0 1 Y N N N N N 23.086 5.914  -22.602 -0.370 2.707  1.618  N3  K9M 8  
K9M C10 C7  C 0 1 N N N N N N 21.032 4.992  -23.457 -2.232 1.645  0.442  C10 K9M 9  
K9M C8  C8  C 0 1 N N N N N N 21.301 2.718  -24.303 -1.615 0.114  -1.318 C8  K9M 10 
K9M C22 C9  C 0 1 Y N N N N N 18.007 3.925  -23.234 -4.689 -0.719 0.035  C22 K9M 11 
K9M C7  C10 C 0 1 N N N N N N 22.423 2.263  -23.354 -0.200 -0.131 -0.788 C7  K9M 12 
K9M C6  C11 C 0 1 Y N N N N N 24.499 3.557  -22.460 1.518  1.134  0.528  C6  K9M 13 
K9M C1  C12 C 0 1 Y N N N N N 23.135 3.543  -22.903 0.174  0.951  0.187  C1  K9M 14 
K9M C4  C13 C 0 1 Y N N N N N 24.366 5.844  -22.218 0.903  2.856  1.921  C4  K9M 15 
K9M C19 C14 C 0 1 Y N N N N N 17.561 3.987  -26.049 -5.690 1.008  -1.905 C19 K9M 16 
K9M C20 C15 C 0 1 Y N N N N N 16.472 4.097  -25.180 -6.527 0.090  -1.347 C20 K9M 17 
K9M C21 C16 C 0 1 Y N N N N N 16.684 4.048  -23.781 -6.044 -0.799 -0.372 C21 K9M 18 
K9M C2  C17 C 0 1 Y N N N N N 22.463 4.800  -23.000 -0.767 1.773  0.760  C2  K9M 19 
K9M N9  N3  N 0 1 N N N N N N 20.412 3.718  -23.624 -2.510 0.342  -0.172 N9  K9M 20 
K9M N11 N4  N 0 1 N N N N N N 25.240 2.394  -22.328 2.500  0.330  -0.027 N11 K9M 21 
K9M N14 N5  N 0 1 N N N N N N 26.747 0.167  -21.448 5.022  -0.720 -0.577 N14 K9M 22 
K9M C23 C18 C 0 1 Y N N N N N 15.582 4.131  -22.897 -6.885 -1.757 0.221  C23 K9M 23 
K9M C24 C19 C 0 1 Y N N N N N 15.812 4.105  -21.491 -6.385 -2.602 1.163  C24 K9M 24 
K9M C25 C20 C 0 1 Y N N N N N 17.115 4.006  -20.923 -5.048 -2.533 1.551  C25 K9M 25 
K9M C26 C21 C 0 1 Y N N N N N 18.216 3.897  -21.819 -4.211 -1.601 1.017  C26 K9M 26 
K9M C27 C22 C 0 1 N N N N N N 27.534 -0.754 -20.804 6.360  -0.878 -0.524 C27 K9M 27 
K9M C28 C23 C 0 1 N N N N N N 28.958 -1.089 -21.364 6.968  -1.814 0.488  C28 K9M 28 
K9M O29 O1  O 0 1 N N N N N N 27.049 -1.285 -19.777 7.074  -0.266 -1.290 O29 K9M 29 
K9M C30 C24 C 0 1 N N N N N N 30.092 -0.589 -20.404 8.491  -1.809 0.337  C30 K9M 30 
K9M H1  H1  H 0 1 N N N N N N 19.713 3.822  -26.186 -3.714 1.833  -1.972 H1  K9M 31 
K9M H2  H2  H 0 1 N N N N N N 26.614 0.495  -23.552 3.855  -0.390 -2.296 H2  K9M 32 
K9M H3  H3  H 0 1 N N N N N N 28.208 0.891  -22.824 5.184  0.774  -2.050 H3  K9M 33 
K9M H4  H4  H 0 1 N N N N N N 27.180 2.842  -21.648 4.018  1.777  -0.151 H4  K9M 34 
K9M H5  H5  H 0 1 N N N N N N 26.943 2.964  -23.425 2.903  1.734  -1.538 H5  K9M 35 
K9M H6  H6  H 0 1 N N N N N N 23.697 1.621  -21.117 2.457  -0.986 1.610  H6  K9M 36 
K9M H7  H7  H 0 1 N N N N N N 24.205 0.563  -22.476 3.763  0.223  1.649  H7  K9M 37 
K9M H8  H8  H 0 1 N N N N N N 25.647 1.081  -19.861 4.737  -1.952 1.105  H8  K9M 38 
K9M H9  H9  H 0 1 N N N N N N 24.955 -0.461 -20.469 3.559  -2.191 -0.211 H9  K9M 39 
K9M H10 H10 H 0 1 N N N N N N 21.022 5.533  -24.415 -2.810 1.740  1.361  H10 K9M 40 
K9M H11 H11 H 0 1 N N N N N N 20.481 5.572  -22.702 -2.522 2.436  -0.250 H11 K9M 41 
K9M H12 H12 H 0 1 N N N N N N 20.702 1.845  -24.601 -1.617 0.991  -1.964 H12 K9M 42 
K9M H13 H13 H 0 1 N N N N N N 21.747 3.178  -25.197 -1.952 -0.758 -1.878 H13 K9M 43 
K9M H14 H14 H 0 1 N N N N N N 22.000 1.734  -22.487 -0.163 -1.099 -0.288 H14 K9M 44 
K9M H15 H15 H 0 1 N N N N N N 23.125 1.600  -23.881 0.504  -0.128 -1.620 H15 K9M 45 
K9M H16 H16 H 0 1 N N N N N N 24.854 6.774  -21.966 1.189  3.625  2.622  H16 K9M 46 
K9M H17 H17 H 0 1 N N N N N N 17.409 3.989  -27.118 -6.068 1.682  -2.659 H17 K9M 47 
K9M H18 H18 H 0 1 N N N N N N 15.474 4.219  -25.574 -7.560 0.040  -1.660 H18 K9M 48 
K9M H19 H19 H 0 1 N N N N N N 14.577 4.213  -23.284 -7.924 -1.821 -0.069 H19 K9M 49 
K9M H20 H20 H 0 1 N N N N N N 14.962 4.163  -20.827 -7.033 -3.337 1.617  H20 K9M 50 
K9M H21 H21 H 0 1 N N N N N N 17.262 4.013  -19.853 -4.676 -3.215 2.301  H21 K9M 51 
K9M H22 H22 H 0 1 N N N N N N 19.217 3.792  -21.427 -3.181 -1.551 1.335  H22 K9M 52 
K9M H23 H23 H 0 1 N N N N N N 29.047 -2.179 -21.483 6.702  -1.487 1.493  H23 K9M 53 
K9M H24 H24 H 0 1 N N N N N N 29.079 -0.602 -22.343 6.590  -2.823 0.323  H24 K9M 54 
K9M H25 H25 H 0 1 N N N N N N 31.073 -0.843 -20.832 8.757  -2.137 -0.668 H25 K9M 55 
K9M H26 H26 H 0 1 N N N N N N 30.016 0.502  -20.283 8.869  -0.800 0.502  H26 K9M 56 
K9M H27 H27 H 0 1 N N N N N N 29.983 -1.075 -19.423 8.931  -2.486 1.069  H27 K9M 57 
# 
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 
K9M C19 C18 DOUB Y N 1  
K9M C19 C20 SING Y N 2  
K9M C18 C17 SING Y N 3  
K9M C20 C21 DOUB Y N 4  
K9M C8  N9  SING N N 5  
K9M C8  C7  SING N N 6  
K9M C17 N9  SING N N 7  
K9M C17 C22 DOUB Y N 8  
K9M C21 C22 SING Y N 9  
K9M C21 C23 SING Y N 10 
K9M N9  C10 SING N N 11 
K9M C10 C2  SING N N 12 
K9M C7  C1  SING N N 13 
K9M C22 C26 SING Y N 14 
K9M C2  C1  DOUB Y N 15 
K9M C2  N3  SING Y N 16 
K9M C1  C6  SING Y N 17 
K9M C23 C24 DOUB Y N 18 
K9M C13 C12 SING N N 19 
K9M C13 N14 SING N N 20 
K9M N3  C4  DOUB Y N 21 
K9M C12 N11 SING N N 22 
K9M C6  N11 SING N N 23 
K9M C6  N5  DOUB Y N 24 
K9M N11 C16 SING N N 25 
K9M C4  N5  SING Y N 26 
K9M C26 C25 DOUB Y N 27 
K9M C16 C15 SING N N 28 
K9M C24 C25 SING Y N 29 
K9M N14 C27 SING N N 30 
K9M N14 C15 SING N N 31 
K9M C28 C27 SING N N 32 
K9M C28 C30 SING N N 33 
K9M C27 O29 DOUB N N 34 
K9M C18 H1  SING N N 35 
K9M C13 H2  SING N N 36 
K9M C13 H3  SING N N 37 
K9M C12 H4  SING N N 38 
K9M C12 H5  SING N N 39 
K9M C16 H6  SING N N 40 
K9M C16 H7  SING N N 41 
K9M C15 H8  SING N N 42 
K9M C15 H9  SING N N 43 
K9M C10 H10 SING N N 44 
K9M C10 H11 SING N N 45 
K9M C8  H12 SING N N 46 
K9M C8  H13 SING N N 47 
K9M C7  H14 SING N N 48 
K9M C7  H15 SING N N 49 
K9M C4  H16 SING N N 50 
K9M C19 H17 SING N N 51 
K9M C20 H18 SING N N 52 
K9M C23 H19 SING N N 53 
K9M C24 H20 SING N N 54 
K9M C25 H21 SING N N 55 
K9M C26 H22 SING N N 56 
K9M C28 H23 SING N N 57 
K9M C28 H24 SING N N 58 
K9M C30 H25 SING N N 59 
K9M C30 H26 SING N N 60 
K9M C30 H27 SING N N 61 
# 
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 
K9M SMILES           ACDLabs              12.01 "c5c(N2Cc3ncnc(N1CCN(CC1)C(=O)CC)c3CC2)c4ccccc4cc5"                                                                                          
K9M InChI            InChI                1.03  "InChI=1S/C24H27N5O/c1-2-23(30)27-12-14-28(15-13-27)24-20-10-11-29(16-21(20)25-17-26-24)22-9-5-7-18-6-3-4-8-19(18)22/h3-9,17H,2,10-16H2,1H3" 
K9M InChIKey         InChI                1.03  XUTSLHHFLGGLJU-UHFFFAOYSA-N                                                                                                                  
K9M SMILES_CANONICAL CACTVS               3.385 "CCC(=O)N1CCN(CC1)c2ncnc3CN(CCc23)c4cccc5ccccc45"                                                                                            
K9M SMILES           CACTVS               3.385 "CCC(=O)N1CCN(CC1)c2ncnc3CN(CCc23)c4cccc5ccccc45"                                                                                            
K9M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCC(=O)N1CCN(CC1)c2c3c(ncn2)CN(CC3)c4cccc5c4cccc5"                                                                                          
K9M SMILES           "OpenEye OEToolkits" 2.0.6 "CCC(=O)N1CCN(CC1)c2c3c(ncn2)CN(CC3)c4cccc5c4cccc5"                                                                                          
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
K9M "SYSTEMATIC NAME" ACDLabs              12.01 "1-{4-[7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one" 
K9M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "1-[4-(7-naphthalen-1-yl-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-one"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
K9M "Create component" 2018-11-14 RCSB 
K9M "Initial release"  2018-12-12 RCSB 
K9M "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            K9M 
_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               C30 
_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      ? 
# 
