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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id MTX
_pdbe_chem_comp_drugbank_details.drugbank_id DB00563
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Methotrexate
_pdbe_chem_comp_drugbank_details.description
"Methotrexate is a folate derivative that inhibits several enzymes responsible for nucleotide synthesis.[A180322] This inhibition leads to suppression of inflammation as well as prevention of cell division.[A180322] Because of these effects, methotrexate is often used to treat inflammation caused by arthritis or to control cell division in neoplastic diseases such as breast cancer and non-Hodgkin's lymphoma.[A180322,L7144,L7147,L7150,L7180]  Due to the toxic effects of methotrexate, it is indicated for treatment of some forms of arthritis and severe psoriasis only if first line treatment has failed or patients are intolerant of those treatments.[L7180]  Methotrexate was granted FDA approval on 7 December 1953.[L7198]"
_pdbe_chem_comp_drugbank_details.cas_number 59-05-2
_pdbe_chem_comp_drugbank_details.mechanism_of_action
"Methotrexate enters tissues and is converted to a methotrexate polyglutamate by folylpolyglutamate.[A180322]  Methotrexate's mechanism of action is due to its inhibition of enzymes responsible for nucleotide synthesis including  dihydrofolate reductase, thymidylate synthase, aminoimidazole caboxamide ribonucleotide transformylase (AICART), and amido phosphoribosyltransferase.[A180322] Inhibtion of nucleotide synthesis prevents cell division.  In rheumatoid arthritis, methotrexate polyglutamates inhibit AICART more than methotrexate.[A180322] This inhibition leads to accumulation of AICART ribonucleotide, which inhibits adenosine deaminase, leading to an accumulation of adenosine triphosphate and adenosine in the extracellular space, stimulating adenosine receptors, leading to anti-inflammatory action.[A180322]"
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
MTX '4-amino-10-methylfolic acid' DrugBank ?
MTX '4-amino-N(10)-methylpteroylglutamic acid' DrugBank ?
MTX Alpha-Methopterin DrugBank ?
MTX Amethopterin DrugBank ?
MTX Methotrexate DrugBank ?
MTX Methotrexatum DrugBank ?
MTX methylaminopterin DrugBank ?
MTX MTX DrugBank ?
MTX 'N-[4-[[(2,4-diamino-6-pteridinyl)methyl]methylamino]benzoyl]-L-glutamic acid' DrugBank ?
MTX Abitrexate DrugBank 'International brand'
MTX Alltrex DrugBank 'International brand'
MTX Artrait DrugBank 'International brand'
MTX Atrexel DrugBank 'International brand'
MTX Bendatrexat DrugBank 'International brand'
MTX Carditrex DrugBank 'International brand'
MTX Dermotrex DrugBank 'International brand'
MTX Ebetrex DrugBank 'International brand'
MTX Emtexate DrugBank 'International brand'
MTX Folex DrugBank 'International brand'
MTX Ledertrexate DrugBank 'International brand'
MTX Maxtrex DrugBank 'International brand'
MTX Meisusheng DrugBank 'International brand'
MTX Mexate DrugBank 'International brand'
MTX Rheumatrex DrugBank 'International brand'
MTX Trexan DrugBank 'International brand'
MTX Zexate DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id MTX
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00563
_pdbe_chem_comp_drugbank_classification.parent 'Glutamic acid and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as glutamic acid and derivatives. These are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
MTX DB00563 'Thymidylate synthase' Humans P04818 yes 1
MTX DB00563 'Bifunctional purine biosynthesis protein ATIC' Humans P31939 yes 2
MTX DB00563 'Dihydrofolate reductase' Humans P00374 yes 3
MTX DB00563 'Reduced folate transporter' Humans P41440 unknown 4
MTX DB00563 'Proton-coupled folate transporter' Humans Q96NT5 unknown 5
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
MTX N1 N 6.404 4.916 1
MTX C2 C 5.104 4.166 2
MTX NA2 N 3.805 4.916 3
MTX N3 N 5.104 2.666 4
MTX C4 C 6.404 1.916 5
MTX NA4 N 6.404 0.416 6
MTX C4A C 7.702 2.666 7
MTX N5 N 9.043 1.864 8
MTX C6 C 10.402 2.635 9
MTX C7 C 10.402 4.197 10
MTX N8 N 9.043 4.968 11
MTX C8A C 7.702 4.166 12
MTX C9 C 11.699 1.879 13
MTX N10 N 13.001 2.624 14
MTX CM C 13.006 4.124 15
MTX C11 C 16.889 0.359 16
MTX C12 C 15.587 -0.386 17
MTX C13 C 14.291 0.369 18
MTX C14 C 14.297 1.869 19
MTX C15 C 15.599 2.614 20
MTX C16 C 16.895 1.859 21
MTX C C 18.185 -0.396 22
MTX O O 18.179 -1.896 23
MTX N N 19.487 0.349 24
MTX CA C 20.783 -0.406 25
MTX CT C 22.085 0.339 26
MTX O1 O 23.381 -0.416 27
MTX O2 O 22.091 1.839 28
MTX CB C 20.777 -1.906 29
MTX CG C 22.074 -2.661 30
MTX CD C 22.068 -4.161 31
MTX OE1 O 23.364 -4.916 32
MTX OE2 O 20.766 -4.906 33
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
MTX N1 C2 DOUBLE NONE 1
MTX N1 C8A SINGLE NONE 2
MTX C2 NA2 SINGLE NONE 3
MTX C2 N3 SINGLE NONE 4
MTX N3 C4 DOUBLE NONE 5
MTX C4 NA4 SINGLE NONE 6
MTX C4 C4A SINGLE NONE 7
MTX C4A N5 SINGLE NONE 8
MTX C4A C8A DOUBLE NONE 9
MTX N5 C6 DOUBLE NONE 10
MTX C6 C7 SINGLE NONE 11
MTX C6 C9 SINGLE NONE 12
MTX C7 N8 DOUBLE NONE 13
MTX N8 C8A SINGLE NONE 14
MTX C9 N10 SINGLE NONE 15
MTX N10 CM SINGLE NONE 16
MTX N10 C14 SINGLE NONE 17
MTX C11 C12 DOUBLE NONE 18
MTX C11 C16 SINGLE NONE 19
MTX C11 C SINGLE NONE 20
MTX C12 C13 SINGLE NONE 21
MTX C13 C14 DOUBLE NONE 22
MTX C14 C15 SINGLE NONE 23
MTX C15 C16 DOUBLE NONE 24
MTX C O DOUBLE NONE 25
MTX C N SINGLE NONE 26
MTX N CA SINGLE NONE 27
MTX CA CT SINGLE NONE 28
MTX CA CB SINGLE BEGINDASH 29
MTX CT O1 DOUBLE NONE 30
MTX CT O2 SINGLE NONE 31
MTX CB CG SINGLE NONE 32
MTX CG CD SINGLE NONE 33
MTX CD OE1 DOUBLE NONE 34
MTX CD OE2 SINGLE NONE 35
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
MTX MurckoScaffold S1 scaffold c1ccc(NCc2cnc3ncncc3n2)cc1 InChI=1S/C13H11N5/c1-2-4-10(5-3-1)15-6-11-7-16-13-12(18-11)8-14-9-17-13/h1-5,7-9,15H,6H2 XASAJMYKOCBVGD-UHFFFAOYSA-N
MTX amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
MTX peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
MTX phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
MTX pteridine F4 fragment c1cnc2ncncc2n1 InChI=1S/C6H4N4/c1-2-9-6-5(8-1)3-7-4-10-6/h1-4H CPNGPNLZQNNVQM-UHFFFAOYSA-N
MTX pyrazine F5 fragment c1cnccn1 InChI=1S/C4H4N2/c1-2-6-4-3-5-1/h1-4H KYQCOXFCLRTKLS-UHFFFAOYSA-N
MTX pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
MTX Z2856434894 F7 fragment CC(C)NCc1ccc(N(C)C)cc1 InChI=1S/C12H20N2/c1-10(2)13-9-11-5-7-12(8-6-11)14(3)4/h5-8,10,13H,9H2,1-4H3 NZXPKDJRJFKEIC-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
MTX N1 S1 1
MTX C2 S1 1
MTX N3 S1 1
MTX C4 S1 1
MTX C4A S1 1
MTX N5 S1 1
MTX C6 S1 1
MTX C7 S1 1
MTX N8 S1 1
MTX C8A S1 1
MTX C9 S1 1
MTX N10 S1 1
MTX C11 S1 1
MTX C12 S1 1
MTX C13 S1 1
MTX C14 S1 1
MTX C15 S1 1
MTX C16 S1 1
MTX N F1 1
MTX C F1 1
MTX O F1 1
MTX C11 F1 1
MTX O1 F2 1
MTX CT F2 1
MTX CA F2 1
MTX N F2 1
MTX C11 F3 1
MTX C12 F3 1
MTX C13 F3 1
MTX C14 F3 1
MTX C15 F3 1
MTX C16 F3 1
MTX C6 F4 1
MTX N5 F4 1
MTX C4A F4 1
MTX C8A F4 1
MTX N8 F4 1
MTX C7 F4 1
MTX N1 F4 1
MTX C2 F4 1
MTX N3 F4 1
MTX C4 F4 1
MTX C4A F5 1
MTX C8A F5 1
MTX N8 F5 1
MTX C7 F5 1
MTX C6 F5 1
MTX N5 F5 1
MTX C4A F6 1
MTX C4 F6 1
MTX N3 F6 1
MTX C2 F6 1
MTX N1 F6 1
MTX C8A F6 1
MTX CT F7 1
MTX CA F7 1
MTX CB F7 1
MTX N F7 1
MTX C F7 1
MTX C11 F7 1
MTX C12 F7 1
MTX C13 F7 1
MTX C14 F7 1
MTX C15 F7 1
MTX C16 F7 1
MTX N10 F7 1
MTX C9 F7 1
MTX CM F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MTX
_pdbe_chem_comp_rdkit_properties.exactmw 454.171
_pdbe_chem_comp_rdkit_properties.amw 454.447
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 13
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 12
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 33
_pdbe_chem_comp_rdkit_properties.NumAtoms 55
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 218.404
_pdbe_chem_comp_rdkit_properties.tpsa 210.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.411
_pdbe_chem_comp_rdkit_properties.CrippenMR 113.052
_pdbe_chem_comp_rdkit_properties.chi0v 15.619
_pdbe_chem_comp_rdkit_properties.chi1v 8.125
_pdbe_chem_comp_rdkit_properties.chi2v 3.283
_pdbe_chem_comp_rdkit_properties.chi3v 3.283
_pdbe_chem_comp_rdkit_properties.chi4v 1.970
_pdbe_chem_comp_rdkit_properties.chi0n 37.619
_pdbe_chem_comp_rdkit_properties.chi1n 18.677
_pdbe_chem_comp_rdkit_properties.chi2n 3.283
_pdbe_chem_comp_rdkit_properties.chi3n 3.283
_pdbe_chem_comp_rdkit_properties.chi4n 1.970
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -4.550
_pdbe_chem_comp_rdkit_properties.kappa1 7.792
_pdbe_chem_comp_rdkit_properties.kappa2 9.720
_pdbe_chem_comp_rdkit_properties.kappa3 5.782
_pdbe_chem_comp_rdkit_properties.Phi 2.295
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
MTX UniChem DrugBank DB00563
MTX UniChem 'Guide to Pharmacology' 4674
MTX UniChem 'Guide to Pharmacology' 4815
MTX UniChem 'PubChem DOTF' 22395177
MTX UniChem 'KEGG LIGAND' C01937
MTX UniChem ChEBI 44185
MTX UniChem ZINC ZINC000001529323
MTX UniChem eMolecules 476359
MTX UniChem fdasrs YL5FZ2Y5U1
MTX UniChem PharmGKB PA450428
MTX UniChem HMDB HMDB0014703
MTX UniChem Selleck Abitrexate
MTX UniChem NMRShiftDB 80020728
MTX UniChem LINCS LSM-5690
MTX UniChem ACTor 51865-79-3
MTX UniChem Nikkaji J2.334E
MTX UniChem BindingDb 18050
MTX UniChem DrugCentral 1751
MTX UniChem BRENDA 132028
MTX UniChem BRENDA 138514
MTX UniChem BRENDA 220748
MTX UniChem BRENDA 229641
MTX UniChem BRENDA 229642
MTX UniChem BRENDA 241
MTX UniChem BRENDA 3613
MTX UniChem BRENDA 39751
MTX UniChem BRENDA 49198
MTX UniChem BRENDA 91627
MTX UniChem BRENDA 9550
MTX UniChem ChemicalBook CB2704227
MTX UniChem ChemicalBook CB2739302
MTX UniChem DailyMed METHOTREXATE
MTX UniChem ClinicalTrials ABITREXATE
MTX UniChem ClinicalTrials ADX-2191
MTX UniChem ClinicalTrials 'CL 14377'
MTX UniChem ClinicalTrials CL-14377
MTX UniChem ClinicalTrials FOLEX
MTX UniChem ClinicalTrials METHOTREXATE
MTX UniChem ClinicalTrials 'METHOTREXATE SODIUM'
MTX UniChem ClinicalTrials MEXATE
MTX UniChem ClinicalTrials NSC-740
MTX UniChem ClinicalTrials RASUVO
MTX UniChem ClinicalTrials TREXALL
MTX UniChem ClinicalTrials XATMEP
MTX UniChem rxnorm METHOTREXATE
MTX UniChem rxnorm 'METHOTREXATE SODIUM'
MTX UniChem rxnorm OTREXUP
MTX UniChem rxnorm RASUVO
MTX UniChem rxnorm REDITREX
MTX UniChem rxnorm TREXALL
MTX UniChem rxnorm XATMEP
MTX UniChem MedChemExpress HY-14519
MTX UniChem 'Probes And Drugs' PD002823
MTX UniChem CCDC DOJZAD
MTX UniChem 'EPA CompTox Dashboard' DTXSID4020822
MTX UniChem SureChEMBL SCHEMBL3711
MTX UniChem 'PubChem TPHARMA' 14760074
MTX UniChem 'PubChem TPHARMA' 14808762
MTX UniChem PubChem 126941
MTX UniChem Mcule MCULE-6523054194
MTX UniChem BindingDb 66082
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
MTX N1 6.974 -1.278 -0.417 ETKDGv3 1
MTX C2 6.637 -2.487 -0.069 ETKDGv3 2
MTX NA2 7.644 -3.437 0.274 ETKDGv3 3
MTX N3 5.249 -2.866 -0.028 ETKDGv3 4
MTX C4 4.307 -2.021 -0.336 ETKDGv3 5
MTX NA4 2.940 -2.431 -0.281 ETKDGv3 6
MTX C4A 4.673 -0.646 -0.735 ETKDGv3 7
MTX N5 3.680 0.332 -1.084 ETKDGv3 8
MTX C6 4.015 1.541 -1.435 ETKDGv3 9
MTX C7 5.451 1.911 -1.460 ETKDGv3 10
MTX N8 6.351 1.025 -1.143 ETKDGv3 11
MTX C8A 5.974 -0.309 -0.765 ETKDGv3 12
MTX C9 2.953 2.549 -1.767 ETKDGv3 13
MTX N10 2.248 2.976 -0.548 ETKDGv3 14
MTX CM 2.938 3.893 0.368 ETKDGv3 15
MTX C11 -1.712 1.604 0.442 ETKDGv3 16
MTX C12 -0.886 0.833 -0.287 ETKDGv3 17
MTX C13 0.469 1.305 -0.637 ETKDGv3 18
MTX C14 0.911 2.512 -0.228 ETKDGv3 19
MTX C15 -0.003 3.355 0.591 ETKDGv3 20
MTX C16 -1.231 2.928 0.906 ETKDGv3 21
MTX C -3.070 1.145 0.821 ETKDGv3 22
MTX O -3.620 1.637 1.844 ETKDGv3 23
MTX N -3.776 0.169 0.034 ETKDGv3 24
MTX CA -5.019 -0.452 0.503 ETKDGv3 25
MTX CT -4.698 -1.402 1.623 ETKDGv3 26
MTX O1 -5.187 -1.214 2.769 ETKDGv3 27
MTX O2 -3.851 -2.483 1.398 ETKDGv3 28
MTX CB -5.726 -1.177 -0.664 ETKDGv3 29
MTX CG -7.171 -1.600 -0.345 ETKDGv3 30
MTX CD -7.228 -2.810 0.537 ETKDGv3 31
MTX OE1 -7.739 -2.731 1.686 ETKDGv3 32
MTX OE2 -6.721 -4.024 0.084 ETKDGv3 33
MTX HN21 7.378 -4.407 0.554 ETKDGv3 34
MTX HN22 8.654 -3.174 0.248 ETKDGv3 35
MTX HN41 2.169 -1.769 -0.519 ETKDGv3 36
MTX HN42 2.693 -3.405 0.002 ETKDGv3 37
MTX H7 5.759 2.910 -1.739 ETKDGv3 38
MTX H91 3.408 3.436 -2.258 ETKDGv3 39
MTX H92 2.248 2.123 -2.512 ETKDGv3 40
MTX HM1 2.890 3.498 1.405 ETKDGv3 41
MTX HM2 4.008 4.008 0.092 ETKDGv3 42
MTX HM3 2.468 4.897 0.325 ETKDGv3 43
MTX H12 -1.177 -0.159 -0.606 ETKDGv3 44
MTX H13 1.096 0.638 -1.209 ETKDGv3 45
MTX H15 0.309 4.332 0.934 ETKDGv3 46
MTX H16 -1.877 3.566 1.496 ETKDGv3 47
MTX HN -3.411 -0.078 -0.914 ETKDGv3 48
MTX HA -5.698 0.349 0.873 ETKDGv3 49
MTX HO2 -3.626 -3.130 2.144 ETKDGv3 50
MTX HB1 -5.775 -0.474 -1.525 ETKDGv3 51
MTX HB2 -5.130 -2.054 -1.001 ETKDGv3 52
MTX HG1 -7.724 -0.755 0.120 ETKDGv3 53
MTX HG2 -7.688 -1.849 -1.296 ETKDGv3 54
MTX HOE2 -6.750 -4.850 0.670 ETKDGv3 55
#