data_A1D9R
# 
_chem_comp.id                                    A1D9R 
_chem_comp.name                                  "(2~{S})-2-[[6-methoxy-2-[(2-methyl-3-phenyl-phenyl)amino]pyrimidin-4-yl]methylamino]-3-oxidanyl-propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H24 N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-09 
_chem_comp.pdbx_modified_date                    2025-03-07 
_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                        408.450 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9R 
_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        9INU 
_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 
A1D9R C10 C1  C 0 1 Y N N N N N 2.242  24.817 6.494 -2.285 1.814  -0.907 C10 A1D9R 1  
A1D9R C13 C2  C 0 1 N N N N N N 3.610  23.500 3.211 -2.841 -1.888 -0.338 C13 A1D9R 2  
A1D9R C15 C3  C 0 1 Y N N N N N -0.128 23.621 4.790 0.344  0.684  -0.695 C15 A1D9R 3  
A1D9R C17 C4  C 0 1 Y N N N N N -2.282 23.025 4.175 1.235  2.563  0.297  C17 A1D9R 4  
A1D9R C21 C5  C 0 1 N N N N N N -2.420 26.285 6.022 3.997  0.405  -1.113 C21 A1D9R 5  
A1D9R C24 C6  C 0 1 N N N N N N -4.546 26.609 3.671 5.989  -2.409 0.222  C24 A1D9R 6  
A1D9R C01 C7  C 0 1 Y N N N N N 8.069  25.377 2.777 -7.555 -2.495 0.833  C01 A1D9R 7  
A1D9R C02 C8  C 0 1 Y N N N N N 7.982  24.476 3.824 -7.304 -1.367 1.594  C02 A1D9R 8  
A1D9R C03 C9  C 0 1 Y N N N N N 6.808  24.377 4.552 -6.269 -0.519 1.254  C03 A1D9R 9  
A1D9R C04 C10 C 0 1 Y N N N N N 5.720  25.175 4.233 -5.477 -0.801 0.143  C04 A1D9R 10 
A1D9R C05 C11 C 0 1 Y N N N N N 5.811  26.081 3.187 -5.734 -1.939 -0.619 C05 A1D9R 11 
A1D9R C06 C12 C 0 1 Y N N N N N 6.985  26.179 2.457 -6.768 -2.783 -0.267 C06 A1D9R 12 
A1D9R C07 C13 C 0 1 Y N N N N N 4.556  25.057 4.978 -4.363 0.107  -0.227 C07 A1D9R 13 
A1D9R C08 C14 C 0 1 Y N N N N N 4.442  25.730 6.184 -4.586 1.479  -0.333 C08 A1D9R 14 
A1D9R C09 C15 C 0 1 Y N N N N N 3.287  25.613 6.940 -3.550 2.323  -0.678 C09 A1D9R 15 
A1D9R C11 C16 C 0 1 Y N N N N N 2.352  24.143 5.286 -2.052 0.448  -0.797 C11 A1D9R 16 
A1D9R C12 C17 C 0 1 Y N N N N N 3.510  24.258 4.535 -3.090 -0.407 -0.457 C12 A1D9R 17 
A1D9R C18 C18 C 0 1 Y N N N N N -2.746 24.152 4.761 2.513  2.119  -0.041 C18 A1D9R 18 
A1D9R C19 C19 C 0 1 Y N N N N N -1.890 25.011 5.363 2.636  0.925  -0.726 C19 A1D9R 19 
A1D9R C23 C20 C 0 1 N N S N N N -4.399 27.272 5.041 5.796  -1.067 -0.436 C23 A1D9R 20 
A1D9R C25 C21 C 0 1 N N N N N N -3.489 28.497 4.926 6.874  -0.098 0.055  C25 A1D9R 21 
A1D9R C30 C22 C 0 1 N N N N N N -2.597 20.960 3.091 -0.273 4.114  1.275  C30 A1D9R 22 
A1D9R N14 N1  N 0 1 N N N N N N 1.288  23.289 4.782 -0.772 -0.064 -1.031 N14 A1D9R 23 
A1D9R N16 N2  N 0 1 Y N N N N N -0.988 22.766 4.193 0.185  1.826  -0.043 N16 A1D9R 24 
A1D9R N20 N3  N 0 1 Y N N N N N -0.595 24.747 5.375 1.546  0.237  -1.030 N20 A1D9R 25 
A1D9R N22 N4  N 0 1 N N N N N N -3.875 26.303 5.999 4.469  -0.539 -0.092 N22 A1D9R 26 
A1D9R O26 O1  O 0 1 N N N N N N -4.105 29.469 4.127 6.848  -0.041 1.482  O26 A1D9R 27 
A1D9R O27 O2  O 0 1 N N N N N N -3.668 26.785 2.788 5.111  -2.877 0.908  O27 A1D9R 28 
A1D9R O28 O3  O 0 1 N N N N N N -5.542 25.879 3.426 7.136  -3.084 0.046  O28 A1D9R 29 
A1D9R O29 O4  O 0 1 N N N N N N -3.178 22.145 3.556 1.068  3.730  0.965  O29 A1D9R 30 
A1D9R H1  H1  H 0 1 N N N N N N 1.344  24.722 7.086 -1.478 2.478  -1.176 H1  A1D9R 31 
A1D9R H2  H2  H 0 1 N N N N N N 4.041  22.504 3.390 -3.009 -2.365 -1.303 H2  A1D9R 32 
A1D9R H3  H3  H 0 1 N N N N N N 2.606  23.392 2.774 -1.811 -2.059 -0.023 H3  A1D9R 33 
A1D9R H4  H4  H 0 1 N N N N N N 4.254  24.059 2.516 -3.522 -2.313 0.400  H4  A1D9R 34 
A1D9R H5  H5  H 0 1 N N N N N N -2.074 26.324 7.065 3.932  -0.103 -2.075 H5  A1D9R 35 
A1D9R H6  H6  H 0 1 N N N N N N -2.038 27.161 5.476 4.696  1.238  -1.189 H6  A1D9R 36 
A1D9R H7  H7  H 0 1 N N N N N N 8.984  25.455 2.208 -8.365 -3.156 1.103  H7  A1D9R 37 
A1D9R H8  H8  H 0 1 N N N N N N 8.827  23.852 4.073 -7.919 -1.149 2.454  H8  A1D9R 38 
A1D9R H9  H9  H 0 1 N N N N N N 6.740  23.676 5.371 -6.075 0.362  1.848  H9  A1D9R 39 
A1D9R H10 H10 H 0 1 N N N N N N 4.968  26.710 2.942 -5.122 -2.162 -1.480 H10 A1D9R 40 
A1D9R H11 H11 H 0 1 N N N N N N 7.055  26.880 1.639 -6.968 -3.665 -0.857 H11 A1D9R 41 
A1D9R H12 H12 H 0 1 N N N N N N 5.256  26.347 6.535 -5.571 1.882  -0.146 H12 A1D9R 42 
A1D9R H13 H13 H 0 1 N N N N N N 3.200  26.142 7.878 -3.727 3.385  -0.768 H13 A1D9R 43 
A1D9R H14 H14 H 0 1 N N N N N N -3.804 24.368 4.749 3.386  2.697  0.222  H14 A1D9R 44 
A1D9R H15 H15 H 0 1 N N N N N N -5.393 27.609 5.372 5.873  -1.178 -1.518 H15 A1D9R 45 
A1D9R H16 H16 H 0 1 N N N N N N -2.533 28.201 4.470 7.852  -0.444 -0.278 H16 A1D9R 46 
A1D9R H17 H17 H 0 1 N N N N N N -3.304 28.911 5.928 6.682  0.895  -0.352 H17 A1D9R 47 
A1D9R H18 H18 H 0 1 N N N N N N -3.369 20.332 2.622 -0.843 4.221  0.352  H18 A1D9R 48 
A1D9R H19 H19 H 0 1 N N N N N N -1.819 21.199 2.351 -0.734 3.350  1.901  H19 A1D9R 49 
A1D9R H20 H20 H 0 1 N N N N N N -2.146 20.417 3.935 -0.265 5.065  1.808  H20 A1D9R 50 
A1D9R H21 H21 H 0 1 N N N N N N 1.551  22.403 4.400 -0.666 -0.943 -1.427 H21 A1D9R 51 
A1D9R H22 H22 H 0 1 N N N N N N -4.209 26.539 6.912 3.806  -1.287 0.043  H22 A1D9R 52 
A1D9R H24 H24 H 0 1 N N N N N N -3.538 30.228 4.057 7.507  0.555  1.864  H24 A1D9R 53 
A1D9R H25 H25 H 0 1 N N N N N N -5.478 25.542 2.540 7.213  -3.940 0.488  H25 A1D9R 54 
# 
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 
A1D9R C06 C01 DOUB Y N 1  
A1D9R C06 C05 SING Y N 2  
A1D9R C01 C02 SING Y N 3  
A1D9R O27 C24 DOUB N N 4  
A1D9R C30 O29 SING N N 5  
A1D9R C05 C04 DOUB Y N 6  
A1D9R C13 C12 SING N N 7  
A1D9R O28 C24 SING N N 8  
A1D9R O29 C17 SING N N 9  
A1D9R C24 C23 SING N N 10 
A1D9R C02 C03 DOUB Y N 11 
A1D9R O26 C25 SING N N 12 
A1D9R C17 N16 DOUB Y N 13 
A1D9R C17 C18 SING Y N 14 
A1D9R N16 C15 SING Y N 15 
A1D9R C04 C03 SING Y N 16 
A1D9R C04 C07 SING N N 17 
A1D9R C12 C07 DOUB Y N 18 
A1D9R C12 C11 SING Y N 19 
A1D9R C18 C19 DOUB Y N 20 
A1D9R N14 C15 SING N N 21 
A1D9R N14 C11 SING N N 22 
A1D9R C15 N20 DOUB Y N 23 
A1D9R C25 C23 SING N N 24 
A1D9R C07 C08 SING Y N 25 
A1D9R C23 N22 SING N N 26 
A1D9R C11 C10 DOUB Y N 27 
A1D9R C19 N20 SING Y N 28 
A1D9R C19 C21 SING N N 29 
A1D9R N22 C21 SING N N 30 
A1D9R C08 C09 DOUB Y N 31 
A1D9R C10 C09 SING Y N 32 
A1D9R C10 H1  SING N N 33 
A1D9R C13 H2  SING N N 34 
A1D9R C13 H3  SING N N 35 
A1D9R C13 H4  SING N N 36 
A1D9R C21 H5  SING N N 37 
A1D9R C21 H6  SING N N 38 
A1D9R C01 H7  SING N N 39 
A1D9R C02 H8  SING N N 40 
A1D9R C03 H9  SING N N 41 
A1D9R C05 H10 SING N N 42 
A1D9R C06 H11 SING N N 43 
A1D9R C08 H12 SING N N 44 
A1D9R C09 H13 SING N N 45 
A1D9R C18 H14 SING N N 46 
A1D9R C23 H15 SING N N 47 
A1D9R C25 H16 SING N N 48 
A1D9R C25 H17 SING N N 49 
A1D9R C30 H18 SING N N 50 
A1D9R C30 H19 SING N N 51 
A1D9R C30 H20 SING N N 52 
A1D9R N14 H21 SING N N 53 
A1D9R N22 H22 SING N N 54 
A1D9R O26 H24 SING N N 55 
A1D9R O28 H25 SING N N 56 
# 
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 
A1D9R InChI            InChI                1.06  "InChI=1S/C22H24N4O4/c1-14-17(15-7-4-3-5-8-15)9-6-10-18(14)25-22-24-16(11-20(26-22)30-2)12-23-19(13-27)21(28)29/h3-11,19,23,27H,12-13H2,1-2H3,(H,28,29)(H,24,25,26)/t19-/m0/s1" 
A1D9R InChIKey         InChI                1.06  QSHNMTVUJAVARU-IBGZPJMESA-N                                                                                                                                                     
A1D9R SMILES_CANONICAL CACTVS               3.385 "COc1cc(CN[C@@H](CO)C(O)=O)nc(Nc2cccc(c2C)c3ccccc3)n1"                                                                                                                          
A1D9R SMILES           CACTVS               3.385 "COc1cc(CN[CH](CO)C(O)=O)nc(Nc2cccc(c2C)c3ccccc3)n1"                                                                                                                            
A1D9R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(cccc1Nc2nc(cc(n2)OC)CN[C@@H](CO)C(=O)O)c3ccccc3"                                                                                                                          
A1D9R SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(cccc1Nc2nc(cc(n2)OC)CNC(CO)C(=O)O)c3ccccc3"                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           A1D9R 
_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})-2-[[6-methoxy-2-[(2-methyl-3-phenyl-phenyl)amino]pyrimidin-4-yl]methylamino]-3-oxidanyl-propanoic 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 
A1D9R "Create component" 2024-07-09 PDBC 
A1D9R "Initial release"  2025-03-12 RCSB 
# 
