data_YMA
# 
_chem_comp.id                                    YMA 
_chem_comp.name                                  "7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H33 N5 O8 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-10-14 
_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                        511.613 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMA 
_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        1PY0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
YMA O8   O8   O 0 1 N N N N N N 3.600  14.705 2.420  3.174  0.508  1.188   O8   YMA 1  
YMA C2   C2   C 0 1 N N N N N N 3.227  13.510 3.027  3.150  -0.571 0.648   C2   YMA 2  
YMA O7   O7   O 0 1 N N N N N N 2.234  13.477 3.939  4.171  -1.427 0.814   O7   YMA 3  
YMA C1   C1   C 0 1 N N N N N N 3.918  12.189 2.679  1.974  -0.959 -0.210  C1   YMA 4  
YMA N1   N1   N 0 1 N N N N N N 3.202  11.428 1.673  0.930  0.068  -0.104  N1   YMA 5  
YMA C10  C10  C 0 1 N N N N N N 3.530  11.539 0.229  0.058  -0.093 -1.275  C10  YMA 6  
YMA C11  C11  C 0 1 N N N N N N 3.555  13.005 -0.271 0.755  0.475  -2.513  C11  YMA 7  
YMA N3   N3   N 0 1 N N N N N N 2.708  13.294 -1.453 -0.088 0.256  -3.695  N3   YMA 8  
YMA C14  C14  C 0 1 N N N N N N 2.108  14.661 -1.586 0.635  0.822  -4.841  C14  YMA 9  
YMA C15  C15  C 0 1 N N N N N N 0.897  14.763 -2.131 0.014  0.326  -6.122  C15  YMA 10 
YMA N5   N5   N 0 1 N N N N N N 0.766  16.120 -2.221 0.528  0.702  -7.310  N5   YMA 11 
YMA C16  C16  C 0 1 N N N N N N 1.488  17.300 -1.521 -0.075 0.219  -8.554  C16  YMA 12 
YMA C18  C18  C 0 1 N N N N N N 2.802  18.188 -1.061 0.693  0.790  -9.748  C18  YMA 13 
YMA S2   S2   S 0 1 N N N N N N 3.844  18.470 -2.524 -0.054 0.193  -11.289 S2   YMA 14 
YMA O6   O6   O 0 1 N N N N N N 0.041  13.974 -2.369 -0.947 -0.411 -6.083  O6   YMA 15 
YMA C12  C12  C 0 1 N N N N N N 2.535  12.286 -2.527 -1.294 1.074  -3.510  C12  YMA 16 
YMA C13  C13  C 0 1 N N N N N N 1.614  11.176 -2.153 -2.286 0.323  -2.660  C13  YMA 17 
YMA O4   O4   O 0 1 N N N N N N 2.021  9.853  -2.244 -3.399 0.936  -2.229  O4   YMA 18 
YMA O3   O3   O 0 1 N N N N N N 0.387  11.478 -1.713 -2.078 -0.830 -2.367  O3   YMA 19 
YMA C3   C3   C 0 1 N N N N N N 2.153  10.500 2.157  0.121  -0.270 1.073   C3   YMA 20 
YMA C4   C4   C 0 1 N N N N N N 1.005  10.281 1.142  0.905  0.066  2.344   C4   YMA 21 
YMA N2   N2   N 0 1 N N N N N N -0.197 10.323 1.661  0.040  -0.120 3.516   N2   YMA 22 
YMA C5   C5   C 0 1 N N N N N N -0.518 10.508 3.194  -0.249 -1.558 3.602   C5   YMA 23 
YMA C6   C6   C 0 1 N N N N N N -1.287 11.733 3.561  -1.387 -1.897 2.675   C6   YMA 24 
YMA O2   O2   O 0 1 N N N N N N -2.633 11.635 3.880  -1.992 -1.015 2.113   O2   YMA 25 
YMA O1   O1   O 0 1 N N N N N N -0.663 12.923 3.562  -1.729 -3.179 2.473   O1   YMA 26 
YMA C7   C7   C 0 1 N N N N N N -1.471 10.088 0.824  0.848  0.218  4.695   C7   YMA 27 
YMA C8   C8   C 0 1 N N N N N N -2.175 11.565 0.577  -0.052 0.376  5.893   C8   YMA 28 
YMA O5   O5   O 0 1 N N N N N N -1.335 12.677 -0.201 -1.255 0.317  5.759   O5   YMA 29 
YMA N4   N4   N 0 1 N N N N N N -3.029 12.414 1.113  0.480  0.584  7.114   N4   YMA 30 
YMA C9   C9   C 0 1 N N N N N N -3.060 13.960 1.288  -0.395 0.738  8.278   C9   YMA 31 
YMA C17  C17  C 0 1 N N N N N N -2.973 15.136 2.352  0.455  0.961  9.530   C17  YMA 32 
YMA S1   S1   S 0 1 N N N N N N -4.181 15.586 3.655  -0.628 1.152  10.972  S1   YMA 33 
YMA HO7  HO7  H 0 1 N N N N N N 1.979  12.661 4.354  4.926  -1.178 1.365   HO7  YMA 34 
YMA H11  1H1  H 0 1 N N N N N N 4.092  11.576 3.594  2.295  -1.045 -1.248  H11  YMA 35 
YMA H12  2H1  H 0 1 N N N N N N 4.976  12.361 2.372  1.577  -1.916 0.127   H12  YMA 36 
YMA H101 1H10 H 0 0 N N N N N N 2.837  10.919 -0.386 -0.149 -1.151 -1.430  H101 YMA 37 
YMA H102 2H10 H 0 0 N N N N N N 4.490  11.022 -0.003 -0.877 0.440  -1.108  H102 YMA 38 
YMA H111 1H11 H 0 0 N N N N N N 4.606  13.322 -0.469 0.920  1.544  -2.378  H111 YMA 39 
YMA H112 2H11 H 0 0 N N N N N N 3.293  13.697 0.564  1.714  -0.025 -2.652  H112 YMA 40 
YMA H141 1H14 H 0 0 N N N N N N 2.816  15.318 -2.143 1.679  0.513  -4.800  H141 YMA 41 
YMA H142 2H14 H 0 0 N N N N N N 2.102  15.156 -0.587 0.576  1.910  -4.807  H142 YMA 42 
YMA HN5  HN5  H 0 1 N N N N N N 0.026  16.273 -2.906 1.297  1.291  -7.340  HN5  YMA 43 
YMA H161 1H16 H 0 0 N N N N N N 1.057  17.148 -0.504 -1.114 0.543  -8.603  H161 YMA 44 
YMA H162 2H16 H 0 0 N N N N N N 0.926  18.125 -2.017 -0.031 -0.869 -8.581  H162 YMA 45 
YMA H181 1H18 H 0 0 N N N N N N 3.363  17.719 -0.219 1.732  0.466  -9.699  H181 YMA 46 
YMA H182 2H18 H 0 0 N N N N N N 2.520  19.136 -0.546 0.649  1.879  -9.721  H182 YMA 47 
YMA HS2  HS2  H 0 1 N N N N N N 4.600  18.981 -2.259 0.747  0.794  -12.186 HS2  YMA 48 
YMA H121 1H12 H 0 0 N N N N N N 3.522  11.887 -2.857 -1.026 2.009  -3.017  H121 YMA 49 
YMA H122 2H12 H 0 0 N N N N N N 2.205  12.771 -3.475 -1.738 1.291  -4.482  H122 YMA 50 
YMA HO4  HO4  H 0 1 N N N N N N 1.434  9.145  -2.006 -4.036 0.454  -1.683  HO4  YMA 51 
YMA H31  1H3  H 0 1 N N N N N N 1.751  10.838 3.141  -0.109 -1.336 1.061   H31  YMA 52 
YMA H32  2H3  H 0 1 N N N N N N 2.600  9.526  2.464  -0.805 0.302  1.055   H32  YMA 53 
YMA H41  1H4  H 0 1 N N N N N N 1.155  9.325  0.588  1.238  1.103  2.300   H41  YMA 54 
YMA H42  2H4  H 0 1 N N N N N N 1.089  11.007 0.300  1.771  -0.590 2.422   H42  YMA 55 
YMA H51  1H5  H 0 1 N N N N N N 0.426  10.464 3.786  -0.525 -1.813 4.625   H51  YMA 56 
YMA H52  2H5  H 0 1 N N N N N N -1.041 9.603  3.582  0.636  -2.125 3.313   H52  YMA 57 
YMA HO1  HO1  H 0 1 N N N N N N -1.153 13.703 3.796  -2.460 -3.397 1.878   HO1  YMA 58 
YMA H71  1H7  H 0 1 N N N N N N -2.164 9.346  1.284  1.380  1.151  4.515   H71  YMA 59 
YMA H72  2H7  H 0 1 N N N N N N -1.275 9.534  -0.124 1.567  -0.579 4.884   H72  YMA 60 
YMA HN4  HN4  H 0 1 N N N N N N -3.767 11.789 1.437  1.443  0.632  7.221   HN4  YMA 61 
YMA H91  1H9  H 0 1 N N N N N N -4.029 14.203 0.792  -0.996 -0.162 8.403   H91  YMA 62 
YMA H92  2H9  H 0 1 N N N N N N -2.252 14.263 0.581  -1.052 1.595  8.128   H92  YMA 63 
YMA H171 1H17 H 0 0 N N N N N N -2.813 16.066 1.758  1.056  1.862  9.405   H171 YMA 64 
YMA H172 2H17 H 0 0 N N N N N N -2.002 14.990 2.881  1.112  0.104  9.680   H172 YMA 65 
YMA HS1  HS1  H 0 1 N N N N N N -4.129 16.289 4.291  0.293  1.332  11.935  HS1  YMA 66 
# 
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 
YMA O8  C2   DOUB N N 1  
YMA C2  O7   SING N N 2  
YMA C2  C1   SING N N 3  
YMA O7  HO7  SING N N 4  
YMA C1  N1   SING N N 5  
YMA C1  H11  SING N N 6  
YMA C1  H12  SING N N 7  
YMA N1  C10  SING N N 8  
YMA N1  C3   SING N N 9  
YMA C10 C11  SING N N 10 
YMA C10 H101 SING N N 11 
YMA C10 H102 SING N N 12 
YMA C11 N3   SING N N 13 
YMA C11 H111 SING N N 14 
YMA C11 H112 SING N N 15 
YMA N3  C14  SING N N 16 
YMA N3  C12  SING N N 17 
YMA C14 C15  SING N N 18 
YMA C14 H141 SING N N 19 
YMA C14 H142 SING N N 20 
YMA C15 N5   SING N N 21 
YMA C15 O6   DOUB N N 22 
YMA N5  C16  SING N N 23 
YMA N5  HN5  SING N N 24 
YMA C16 C18  SING N N 25 
YMA C16 H161 SING N N 26 
YMA C16 H162 SING N N 27 
YMA C18 S2   SING N N 28 
YMA C18 H181 SING N N 29 
YMA C18 H182 SING N N 30 
YMA S2  HS2  SING N N 31 
YMA C12 C13  SING N N 32 
YMA C12 H121 SING N N 33 
YMA C12 H122 SING N N 34 
YMA C13 O4   SING N N 35 
YMA C13 O3   DOUB N N 36 
YMA O4  HO4  SING N N 37 
YMA C3  C4   SING N N 38 
YMA C3  H31  SING N N 39 
YMA C3  H32  SING N N 40 
YMA C4  N2   SING N N 41 
YMA C4  H41  SING N N 42 
YMA C4  H42  SING N N 43 
YMA N2  C5   SING N N 44 
YMA N2  C7   SING N N 45 
YMA C5  C6   SING N N 46 
YMA C5  H51  SING N N 47 
YMA C5  H52  SING N N 48 
YMA C6  O2   DOUB N N 49 
YMA C6  O1   SING N N 50 
YMA O1  HO1  SING N N 51 
YMA C7  C8   SING N N 52 
YMA C7  H71  SING N N 53 
YMA C7  H72  SING N N 54 
YMA C8  O5   DOUB N N 55 
YMA C8  N4   SING N N 56 
YMA N4  C9   SING N N 57 
YMA N4  HN4  SING N N 58 
YMA C9  C17  SING N N 59 
YMA C9  H91  SING N N 60 
YMA C9  H92  SING N N 61 
YMA C17 S1   SING N N 62 
YMA C17 H171 SING N N 63 
YMA C17 H172 SING N N 64 
YMA S1  HS1  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 
YMA SMILES           ACDLabs              10.04 "O=C(NCCS)CN(CCN(CC(=O)O)CCN(CC(=O)NCCS)CC(=O)O)CC(=O)O"                                                                                                                        
YMA SMILES_CANONICAL CACTVS               3.341 "OC(=O)CN(CCN(CC(O)=O)CC(=O)NCCS)CCN(CC(O)=O)CC(=O)NCCS"                                                                                                                        
YMA SMILES           CACTVS               3.341 "OC(=O)CN(CCN(CC(O)=O)CC(=O)NCCS)CCN(CC(O)=O)CC(=O)NCCS"                                                                                                                        
YMA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CS)NC(=O)CN(CCN(CCN(CC(=O)NCCS)CC(=O)O)CC(=O)O)CC(=O)O"                                                                                                                      
YMA SMILES           "OpenEye OEToolkits" 1.5.0 "C(CS)NC(=O)CN(CCN(CCN(CC(=O)NCCS)CC(=O)O)CC(=O)O)CC(=O)O"                                                                                                                      
YMA InChI            InChI                1.03  "InChI=1S/C18H33N5O8S2/c24-14(19-1-7-32)9-22(12-17(28)29)5-3-21(11-16(26)27)4-6-23(13-18(30)31)10-15(25)20-2-8-33/h32-33H,1-13H2,(H,19,24)(H,20,25)(H,26,27)(H,28,29)(H,30,31)" 
YMA InChIKey         InChI                1.03  MRDWXQKAAKNXSP-UHFFFAOYSA-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 
YMA "SYSTEMATIC NAME" ACDLabs              10.04 "N,N-bis{2-[(carboxymethyl){2-oxo-2-[(2-sulfanylethyl)amino]ethyl}amino]ethyl}glycine"         
YMA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[bis[2-[carboxymethyl-[2-oxo-2-(2-sulfanylethylamino)ethyl]amino]ethyl]amino]ethanoic 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 
YMA "Create component"  2004-10-14 RCSB 
YMA "Modify descriptor" 2011-06-04 RCSB 
YMA "Modify PCM"        2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 YMA CYS None Crosslinker "Amino-acid side chain" "Any position" S1 SG ? ? 
2 YMA CYS None Crosslinker "Amino-acid side chain" "Any position" S2 SG ? ? 
# 
