data_MTX
# 
_chem_comp.id                                    MTX 
_chem_comp.name                                  METHOTREXATE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H22 N8 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        454.439 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     MTX 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        4DFR 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
MTX N1   N1   N 0 1 Y N N N N N 16.724 65.101 45.857 2.395  0.559  5.470  N1   MTX 1  
MTX C2   C2   C 0 1 Y N N N N N 16.136 65.424 47.049 2.310  0.209  6.738  C2   MTX 2  
MTX NA2  NA2  N 0 1 N N N N N N 14.808 64.996 47.270 3.481  0.080  7.461  NA2  MTX 3  
MTX N3   N3   N 0 1 Y N N N N N 16.766 66.078 48.071 1.158  -0.024 7.359  N3   MTX 4  
MTX C4   C4   C 0 1 Y N N N N N 18.001 66.587 47.924 0.000  0.081  6.723  C4   MTX 5  
MTX NA4  NA4  N 0 1 N N N N N N 18.523 67.297 48.888 -1.192 -0.161 7.369  NA4  MTX 6  
MTX C4A  C4A  C 0 1 Y N N N N N 18.630 66.369 46.644 0.031  0.467  5.311  C4A  MTX 7  
MTX N5   N5   N 0 1 Y N N N N N 19.814 66.982 46.490 -1.077 0.604  4.591  N5   MTX 8  
MTX C6   C6   C 0 1 Y N N N N N 20.308 66.821 45.261 -0.989 0.948  3.324  C6   MTX 9  
MTX C7   C7   C 0 1 Y N N N N N 19.725 66.102 44.371 0.253  1.179  2.735  C7   MTX 10 
MTX N8   N8   N 0 1 Y N N N N N 18.560 65.424 44.401 1.363  1.054  3.431  N8   MTX 11 
MTX C8A  C8A  C 0 1 Y N N N N N 17.991 65.747 45.644 1.297  0.701  4.717  C8A  MTX 12 
MTX C9   C9   C 0 1 N N N N N N 21.711 67.394 45.048 -2.244 1.099  2.503  C9   MTX 13 
MTX N10  N10  N 0 1 N N N N N N 22.028 67.717 43.540 -2.574 -0.182 1.875  N10  MTX 14 
MTX CM   CM   C 0 1 N N N N N N 23.296 66.877 43.297 -3.438 -1.138 2.572  CM   MTX 15 
MTX C11  C11  C 0 1 Y N N N N N 19.702 69.969 41.061 -1.056 -1.107 -1.887 C11  MTX 16 
MTX C12  C12  C 0 1 Y N N N N N 20.746 69.211 40.495 -1.881 -2.019 -1.221 C12  MTX 17 
MTX C13  C13  C 0 1 Y N N N N N 21.534 68.508 41.355 -2.381 -1.710 0.022  C13  MTX 18 
MTX C14  C14  C 0 1 Y N N N N N 21.189 68.492 42.724 -2.067 -0.491 0.618  C14  MTX 19 
MTX C15  C15  C 0 1 Y N N N N N 20.168 69.307 43.231 -1.250 0.420  -0.045 C15  MTX 20 
MTX C16  C16  C 0 1 Y N N N N N 19.422 70.099 42.451 -0.742 0.114  -1.286 C16  MTX 21 
MTX C    C    C 0 1 N N N N N N 18.966 70.777 40.090 -0.518 -1.436 -3.221 C    MTX 22 
MTX O    O    O 0 1 N N N N N N 19.469 71.019 39.002 -0.792 -2.500 -3.742 O    MTX 23 
MTX N    N    N 0 1 N N N N N N 17.735 71.051 40.429 0.276  -0.556 -3.862 N    MTX 24 
MTX CA   CA   C 0 1 N N S N N N 16.877 71.923 39.715 0.811  -0.882 -5.186 CA   MTX 25 
MTX CT   CT   C 0 1 N N N N N N 16.397 72.948 40.561 2.135  -1.584 -5.034 CT   MTX 26 
MTX O1   O1   O 0 1 N N N N N N 16.202 72.626 41.863 2.489  -2.392 -5.861 O1   MTX 27 
MTX O2   O2   O 0 1 N N N N N N 15.866 74.111 40.362 2.922  -1.313 -3.981 O2   MTX 28 
MTX CB   CB   C 0 1 N N N N N N 15.656 71.197 39.259 1.005  0.405  -5.989 CB   MTX 29 
MTX CG   CG   C 0 1 N N N N N N 16.080 70.349 37.905 -0.339 1.118  -6.143 CG   MTX 30 
MTX CD   CD   C 0 1 N N N N N N 16.286 70.898 36.272 -0.148 2.386  -6.933 CD   MTX 31 
MTX OE1  OE1  O 0 1 N N N N N N 17.507 70.413 35.853 0.951  2.689  -7.333 OE1  MTX 32 
MTX OE2  OE2  O 0 1 N N N N N N 15.722 72.117 36.236 -1.198 3.180  -7.194 OE2  MTX 33 
MTX HN21 1HN2 H 0 0 N N N N N N 14.369 65.236 48.158 3.448  -0.175 8.396  HN21 MTX 34 
MTX HN22 2HN2 H 0 0 N N N N N N 14.754 63.986 47.133 4.335  0.246  7.033  HN22 MTX 35 
MTX HN41 1HN4 H 0 0 N N N N N N 19.460 67.683 48.776 -1.193 -0.415 8.305  HN41 MTX 36 
MTX HN42 2HN4 H 0 0 N N N N N N 18.497 66.747 49.747 -2.030 -0.078 6.887  HN42 MTX 37 
MTX H7   H7   H 0 1 N N N N N N 20.314 66.060 43.439 0.305  1.464  1.695  H7   MTX 38 
MTX H91  1H9  H 0 1 N N N N N N 21.873 68.292 45.688 -2.084 1.851  1.731  H91  MTX 39 
MTX H92  2H9  H 0 1 N N N N N N 22.485 66.717 45.479 -3.065 1.409  3.149  H92  MTX 40 
MTX HM1  1HM  H 0 1 N N N N N N 23.520 67.105 42.229 -3.735 -0.724 3.535  HM1  MTX 41 
MTX HM2  2HM  H 0 1 N N N N N N 24.133 67.067 44.008 -4.326 -1.331 1.970  HM2  MTX 42 
MTX HM3  3HM  H 0 1 N N N N N N 23.199 65.792 43.538 -2.896 -2.071 2.729  HM3  MTX 43 
MTX H12  H12  H 0 1 N N N N N N 20.940 69.169 39.410 -2.125 -2.964 -1.682 H12  MTX 44 
MTX H13  H13  H 0 1 N N N N N N 22.414 67.974 40.959 -3.018 -2.413 0.538  H13  MTX 45 
MTX H15  H15  H 0 1 N N N N N N 19.937 69.326 44.309 -1.008 1.364  0.419  H15  MTX 46 
MTX H16  H16  H 0 1 N N N N N N 18.671 70.773 42.897 -0.105 0.820  -1.798 H16  MTX 47 
MTX HN   HN   H 0 1 N N N N N N 17.434 70.569 41.276 0.494  0.292  -3.446 HN   MTX 48 
MTX HA   HA   H 0 1 N N N N N N 17.468 72.326 38.860 0.112  -1.535 -5.710 HA   MTX 49 
MTX HO2  HO2  H 0 1 N N N N N N 15.543 74.800 40.930 3.772  -1.763 -3.884 HO2  MTX 50 
MTX HB1  1HB  H 0 1 N N N N N N 15.202 70.558 40.052 1.704  1.057  -5.465 HB1  MTX 51 
MTX HB2  2HB  H 0 1 N N N N N N 14.779 71.868 39.100 1.403  0.162  -6.974 HB2  MTX 52 
MTX HG1  1HG  H 0 1 N N N N N N 17.039 69.843 38.165 -1.038 0.465  -6.666 HG1  MTX 53 
MTX HG2  2HG  H 0 1 N N N N N N 15.343 69.514 37.841 -0.737 1.360  -5.157 HG2  MTX 54 
MTX HOE2 2HOE H 0 0 N N N N N N 15.834 72.417 35.341 -1.075 3.994  -7.701 HOE2 MTX 55 
# 
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 
MTX N1  C2   DOUB Y N 1  
MTX N1  C8A  SING Y N 2  
MTX C2  NA2  SING N N 3  
MTX C2  N3   SING Y N 4  
MTX NA2 HN21 SING N N 5  
MTX NA2 HN22 SING N N 6  
MTX N3  C4   DOUB Y N 7  
MTX C4  NA4  SING N N 8  
MTX C4  C4A  SING Y N 9  
MTX NA4 HN41 SING N N 10 
MTX NA4 HN42 SING N N 11 
MTX C4A N5   SING Y N 12 
MTX C4A C8A  DOUB Y N 13 
MTX N5  C6   DOUB Y N 14 
MTX C6  C7   SING Y N 15 
MTX C6  C9   SING N N 16 
MTX C7  N8   DOUB Y N 17 
MTX C7  H7   SING N N 18 
MTX N8  C8A  SING Y N 19 
MTX C9  N10  SING N N 20 
MTX C9  H91  SING N N 21 
MTX C9  H92  SING N N 22 
MTX N10 CM   SING N N 23 
MTX N10 C14  SING N N 24 
MTX CM  HM1  SING N N 25 
MTX CM  HM2  SING N N 26 
MTX CM  HM3  SING N N 27 
MTX C11 C12  DOUB Y N 28 
MTX C11 C16  SING Y N 29 
MTX C11 C    SING N N 30 
MTX C12 C13  SING Y N 31 
MTX C12 H12  SING N N 32 
MTX C13 C14  DOUB Y N 33 
MTX C13 H13  SING N N 34 
MTX C14 C15  SING Y N 35 
MTX C15 C16  DOUB Y N 36 
MTX C15 H15  SING N N 37 
MTX C16 H16  SING N N 38 
MTX C   O    DOUB N N 39 
MTX C   N    SING N N 40 
MTX N   CA   SING N N 41 
MTX N   HN   SING N N 42 
MTX CA  CT   SING N N 43 
MTX CA  CB   SING N N 44 
MTX CA  HA   SING N N 45 
MTX CT  O1   DOUB N N 46 
MTX CT  O2   SING N N 47 
MTX O2  HO2  SING N N 48 
MTX CB  CG   SING N N 49 
MTX CB  HB1  SING N N 50 
MTX CB  HB2  SING N N 51 
MTX CG  CD   SING N N 52 
MTX CG  HG1  SING N N 53 
MTX CG  HG2  SING N N 54 
MTX CD  OE1  DOUB N N 55 
MTX CD  OE2  SING N N 56 
MTX OE2 HOE2 SING N N 57 
# 
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 
MTX SMILES           ACDLabs              10.04 "O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O"                                                                                                                                               
MTX SMILES_CANONICAL CACTVS               3.341 "CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O"                                                                                                                                          
MTX SMILES           CACTVS               3.341 "CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O"                                                                                                                                            
MTX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O"                                                                                                                                        
MTX SMILES           "OpenEye OEToolkits" 1.5.0 "CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O"                                                                                                                                             
MTX InChI            InChI                1.03  "InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1" 
MTX InChIKey         InChI                1.03  FBOZXECLQNJBKD-ZDUSSCGKSA-N                                                                                                                                                                                
# 
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 
MTX "SYSTEMATIC NAME" ACDLabs              10.04 "N-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)carbonyl]-L-glutamic acid"          
MTX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[[4-[(2,4-diaminopteridin-6-yl)methyl-methyl-amino]phenyl]carbonylamino]pentanedioic 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 
MTX "Create component"  1999-07-08 EBI  
MTX "Modify descriptor" 2011-06-04 RCSB 
MTX "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            MTX 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_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               CD 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
