data_A1L2P
# 
_chem_comp.id                                    A1L2P 
_chem_comp.name                                  "(2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H29 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-03 
_chem_comp.pdbx_modified_date                    2025-06-27 
_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                        447.526 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1L2P 
_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        9IJT 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
A1L2P C32 C1  C 0 1 Y N N N N N 12.626 11.395 22.447 -9.044 -2.077 0.419  C32 A1L2P 1  
A1L2P C31 C2  C 0 1 Y N N N N N 12.138 11.806 21.228 -8.841 -1.096 1.372  C31 A1L2P 2  
A1L2P C33 C3  C 0 1 Y N N N N N 11.827 10.715 23.359 -8.145 -2.235 -0.621 C33 A1L2P 3  
A1L2P C26 C4  C 0 1 Y N N N N N 7.119  9.443  20.049 -4.690 2.667  0.153  C26 A1L2P 4  
A1L2P C30 C5  C 0 1 Y N N N N N 10.830 11.558 20.898 -7.739 -0.268 1.291  C30 A1L2P 5  
A1L2P C34 C6  C 0 1 Y N N N N N 10.519 10.461 23.015 -7.040 -1.413 -0.712 C34 A1L2P 6  
A1L2P C27 C7  C 0 1 Y N N N N N 8.410  9.762  20.408 -5.797 1.846  0.241  C27 A1L2P 7  
A1L2P C25 C8  C 0 1 Y N N N N N 6.062  10.002 20.728 -3.432 2.119  -0.023 C25 A1L2P 8  
A1L2P C12 C9  C 0 1 Y N N N N N 0.839  10.293 23.822 1.914  -0.828 -0.806 C12 A1L2P 9  
A1L2P C29 C10 C 0 1 Y N N N N N 10.023 10.873 21.791 -6.831 -0.423 0.245  C29 A1L2P 10 
A1L2P C28 C11 C 0 1 Y N N N N N 8.644  10.600 21.445 -5.645 0.464  0.152  C28 A1L2P 11 
A1L2P C3  C12 C 0 1 Y N N N N N 6.277  10.885 21.764 -3.276 0.748  -0.112 C3  A1L2P 12 
A1L2P C11 C13 C 0 1 Y N N N N N 0.626  11.565 24.314 2.915  0.122  -0.876 C11 A1L2P 13 
A1L2P C2  C14 C 0 1 Y N N N N N 7.573  11.180 22.128 -4.375 -0.082 -0.025 C2  A1L2P 14 
A1L2P C8  C15 C 0 1 Y N N N N N 1.646  12.471 24.112 2.564  1.467  -0.766 C8  A1L2P 15 
A1L2P C6  C16 C 0 1 Y N N N N N 2.878  10.920 23.044 0.357  0.848  -0.536 C6  A1L2P 16 
A1L2P C22 C17 C 0 1 N N N N N N -0.605 10.695 28.420 5.920  -2.468 -0.269 C22 A1L2P 17 
A1L2P C18 C18 C 0 1 N N N N N N -2.508 13.149 27.178 7.210  0.280  2.063  C18 A1L2P 18 
A1L2P C17 C19 C 0 1 N N N N N N -3.179 11.818 26.901 5.934  1.125  2.046  C17 A1L2P 19 
A1L2P C19 C20 C 0 1 N N N N N N -1.071 13.038 27.671 6.880  -1.139 1.591  C19 A1L2P 20 
A1L2P C16 C21 C 0 1 N N N N N N -2.329 10.752 26.208 5.345  1.123  0.633  C16 A1L2P 21 
A1L2P C20 C22 C 0 1 N N S N N N -0.389 11.722 27.348 6.265  -1.076 0.191  C20 A1L2P 22 
A1L2P C1  C23 C 0 1 N N N N N N 7.855  12.131 23.229 -4.203 -1.576 -0.122 C1  A1L2P 23 
A1L2P C10 C24 C 0 1 N N N N N N 2.600  14.320 24.986 3.071  3.785  -0.707 C10 A1L2P 24 
A1L2P C14 C25 C 0 1 N N N N N N -0.630 11.948 25.017 4.353  -0.287 -1.067 C14 A1L2P 25 
A1L2P C4  C26 C 0 1 N N N N N N 5.078  11.474 22.466 -1.902 0.158  -0.304 C4  A1L2P 26 
A1L2P N13 N1  N 0 1 Y N N N N N 1.957  9.950  23.170 0.660  -0.435 -0.637 N13 A1L2P 27 
A1L2P N7  N2  N 0 1 Y N N N N N 2.798  12.177 23.484 1.287  1.788  -0.598 N7  A1L2P 28 
A1L2P N15 N3  N 0 1 N N N N N N -0.896 11.077 26.156 5.046  -0.257 0.228  N15 A1L2P 29 
A1L2P O24 O1  O 0 1 N N N N N N 0.058  9.681  28.518 4.822  -2.923 -0.050 O24 A1L2P 30 
A1L2P O23 O2  O 0 1 N N N N N N -1.654 10.995 29.227 6.832  -3.204 -0.923 O23 A1L2P 31 
A1L2P O9  O3  O 0 1 N N N N N N 1.375  13.724 24.594 3.513  2.432  -0.829 O9  A1L2P 32 
A1L2P O5  O4  O 0 1 N N N N N N 4.015  10.514 22.381 -0.937 1.210  -0.365 O5  A1L2P 33 
A1L2P H60 H1  H 0 1 N N N N N N 13.654 11.606 22.701 -9.905 -2.725 0.489  H60 A1L2P 34 
A1L2P H59 H2  H 0 1 N N N N N N 12.783 12.323 20.533 -9.545 -0.977 2.182  H59 A1L2P 35 
A1L2P H61 H3  H 0 1 N N N N N N 12.222 10.395 24.312 -8.309 -3.003 -1.363 H61 A1L2P 36 
A1L2P H56 H4  H 0 1 N N N N N N 6.937  8.755  19.236 -4.808 3.738  0.217  H56 A1L2P 37 
A1L2P H58 H5  H 0 1 N N N N N N 10.433 11.894 19.951 -7.582 0.498  2.035  H58 A1L2P 38 
A1L2P H62 H6  H 0 1 N N N N N N 9.875  9.936  23.705 -6.339 -1.538 -1.524 H62 A1L2P 39 
A1L2P H57 H7  H 0 1 N N N N N N 9.240  9.341  19.859 -6.778 2.275  0.379  H57 A1L2P 40 
A1L2P H55 H8  H 0 1 N N N N N N 5.051  9.746  20.446 -2.569 2.765  -0.092 H55 A1L2P 41 
A1L2P H43 H9  H 0 1 N N N N N N 0.074  9.545  23.969 2.150  -1.878 -0.892 H43 A1L2P 42 
A1L2P H51 H10 H 0 1 N N N N N N -2.508 13.735 26.247 7.950  0.723  1.396  H51 A1L2P 43 
A1L2P H50 H11 H 0 1 N N N N N N -3.095 13.677 27.944 7.609  0.243  3.077  H50 A1L2P 44 
A1L2P H48 H12 H 0 1 N N N N N N -3.511 11.405 27.865 5.209  0.704  2.742  H48 A1L2P 45 
A1L2P H49 H13 H 0 1 N N N N N N -4.055 12.012 26.264 6.170  2.148  2.340  H49 A1L2P 46 
A1L2P H53 H14 H 0 1 N N N N N N -0.487 13.848 27.210 7.793  -1.734 1.561  H53 A1L2P 47 
A1L2P H52 H15 H 0 1 N N N N N N -1.073 13.163 28.764 6.170  -1.596 2.281  H52 A1L2P 48 
A1L2P H46 H16 H 0 1 N N N N N N -2.450 9.804  26.753 4.429  1.712  0.620  H46 A1L2P 49 
A1L2P H47 H17 H 0 1 N N N N N N -2.695 10.632 25.178 6.065  1.557  -0.061 H47 A1L2P 50 
A1L2P H21 H18 H 0 1 N N N N N N 0.691  11.902 27.240 6.980  -0.631 -0.500 H21 A1L2P 51 
A1L2P H36 H19 H 0 1 N N N N N N 7.928  13.151 22.824 -4.282 -1.884 -1.164 H36 A1L2P 52 
A1L2P H37 H20 H 0 1 N N N N N N 7.042  12.088 23.968 -3.224 -1.855 0.267  H37 A1L2P 53 
A1L2P H35 H21 H 0 1 N N N N N N 8.805  11.860 23.713 -4.980 -2.070 0.462  H35 A1L2P 54 
A1L2P H42 H22 H 0 1 N N N N N N 2.408  15.330 25.378 2.578  3.922  0.255  H42 A1L2P 55 
A1L2P H40 H23 H 0 1 N N N N N N 3.072  13.707 25.768 3.928  4.455  -0.775 H40 A1L2P 56 
A1L2P H41 H24 H 0 1 N N N N N N 3.271  14.385 24.117 2.369  4.012  -1.510 H41 A1L2P 57 
A1L2P H44 H25 H 0 1 N N N N N N -0.537 12.984 25.374 4.393  -1.296 -1.477 H44 A1L2P 58 
A1L2P H45 H26 H 0 1 N N N N N N -1.470 11.878 24.310 4.839  0.405  -1.755 H45 A1L2P 59 
A1L2P H38 H27 H 0 1 N N N N N N 5.320  11.674 23.520 -1.669 -0.501 0.532  H38 A1L2P 60 
A1L2P H39 H28 H 0 1 N N N N N N 4.778  12.411 21.975 -1.878 -0.411 -1.234 H39 A1L2P 61 
A1L2P H54 H30 H 0 1 N N N N N N -1.776 10.298 29.861 6.565  -4.092 -1.199 H54 A1L2P 62 
# 
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 
A1L2P C32 C31 DOUB Y N 1  
A1L2P C32 C33 SING Y N 2  
A1L2P C31 C30 SING Y N 3  
A1L2P C33 C34 DOUB Y N 4  
A1L2P C26 C27 DOUB Y N 5  
A1L2P C26 C25 SING Y N 6  
A1L2P C30 C29 DOUB Y N 7  
A1L2P C34 C29 SING Y N 8  
A1L2P C27 C28 SING Y N 9  
A1L2P C25 C3  DOUB Y N 10 
A1L2P C12 C11 DOUB Y N 11 
A1L2P C12 N13 SING Y N 12 
A1L2P C29 C28 SING N N 13 
A1L2P C28 C2  DOUB Y N 14 
A1L2P C3  C2  SING Y N 15 
A1L2P C3  C4  SING N N 16 
A1L2P C11 C8  SING Y N 17 
A1L2P C11 C14 SING N N 18 
A1L2P C2  C1  SING N N 19 
A1L2P C8  N7  DOUB Y N 20 
A1L2P C8  O9  SING N N 21 
A1L2P C6  N13 DOUB Y N 22 
A1L2P C6  N7  SING Y N 23 
A1L2P C6  O5  SING N N 24 
A1L2P C22 C20 SING N N 25 
A1L2P C22 O24 DOUB N N 26 
A1L2P C22 O23 SING N N 27 
A1L2P C18 C17 SING N N 28 
A1L2P C18 C19 SING N N 29 
A1L2P C17 C16 SING N N 30 
A1L2P C19 C20 SING N N 31 
A1L2P C16 N15 SING N N 32 
A1L2P C20 N15 SING N N 33 
A1L2P C10 O9  SING N N 34 
A1L2P C14 N15 SING N N 35 
A1L2P C4  O5  SING N N 36 
A1L2P C32 H60 SING N N 37 
A1L2P C31 H59 SING N N 38 
A1L2P C33 H61 SING N N 39 
A1L2P C26 H56 SING N N 40 
A1L2P C30 H58 SING N N 41 
A1L2P C34 H62 SING N N 42 
A1L2P C27 H57 SING N N 43 
A1L2P C25 H55 SING N N 44 
A1L2P C12 H43 SING N N 45 
A1L2P C18 H51 SING N N 46 
A1L2P C18 H50 SING N N 47 
A1L2P C17 H48 SING N N 48 
A1L2P C17 H49 SING N N 49 
A1L2P C19 H53 SING N N 50 
A1L2P C19 H52 SING N N 51 
A1L2P C16 H46 SING N N 52 
A1L2P C16 H47 SING N N 53 
A1L2P C20 H21 SING N N 54 
A1L2P C1  H36 SING N N 55 
A1L2P C1  H37 SING N N 56 
A1L2P C1  H35 SING N N 57 
A1L2P C10 H42 SING N N 58 
A1L2P C10 H40 SING N N 59 
A1L2P C10 H41 SING N N 60 
A1L2P C14 H44 SING N N 61 
A1L2P C14 H45 SING N N 62 
A1L2P C4  H38 SING N N 63 
A1L2P C4  H39 SING N N 64 
A1L2P O23 H54 SING N N 65 
# 
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 
A1L2P InChI            InChI                1.06  "InChI=1S/C26H29N3O4/c1-18-20(11-8-12-22(18)19-9-4-3-5-10-19)17-33-26-27-15-21(24(28-26)32-2)16-29-14-7-6-13-23(29)25(30)31/h3-5,8-12,15,23H,6-7,13-14,16-17H2,1-2H3,(H,30,31)/t23-/m0/s1" 
A1L2P InChIKey         InChI                1.06  ANUJMSZHAOMHOI-QHCPKHFHSA-N                                                                                                                                                                
A1L2P SMILES_CANONICAL CACTVS               3.385 "COc1nc(OCc2cccc(c2C)c3ccccc3)ncc1CN4CCCC[C@H]4C(O)=O"                                                                                                                                     
A1L2P SMILES           CACTVS               3.385 "COc1nc(OCc2cccc(c2C)c3ccccc3)ncc1CN4CCCC[CH]4C(O)=O"                                                                                                                                      
A1L2P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(cccc1c2ccccc2)COc3ncc(c(n3)OC)CN4CCCC[C@H]4C(=O)O"                                                                                                                                   
A1L2P SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(cccc1c2ccccc2)COc3ncc(c(n3)OC)CN4CCCCC4C(=O)O"                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           A1L2P 
_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        "(2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1L2P "Create component" 2024-07-03 PDBJ 
A1L2P "Initial release"  2025-07-02 RCSB 
# 
