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 ? #