data_YMY
# 
_chem_comp.id                                    YMY 
_chem_comp.name                                  "(1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)methoxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H43 N3 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-03-12 
_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                        533.679 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMY 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7LZT 
_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 
YMY C13 C1  C 0 1 N N S N N N 10.330 4.940  22.099 0.766   0.129  0.998  C13 YMY 1  
YMY C15 C2  C 0 1 N N N N N N 12.434 4.525  23.423 -0.162  -0.932 3.061  C15 YMY 2  
YMY C21 C3  C 0 1 N N N N N N 9.071  9.700  22.147 -4.003  0.789  0.756  C21 YMY 3  
YMY C22 C4  C 0 1 N N N N N N 9.811  10.995 22.592 -5.209  0.520  -0.147 C22 YMY 4  
YMY C24 C5  C 0 1 N N N N N N 9.727  13.503 22.444 -6.641  -1.257 -1.163 C24 YMY 5  
YMY C01 C6  C 0 1 N N R N N N 7.587  2.008  19.521 4.057   1.553  -1.411 C01 YMY 6  
YMY C03 C7  C 0 1 N N S N N N 7.461  3.463  19.967 4.286   0.358  -0.484 C03 YMY 7  
YMY C04 C8  C 0 1 N N N N N N 6.957  4.378  18.823 4.359   -0.925 -1.314 C04 YMY 8  
YMY C05 C9  C 0 1 N N S N N N 6.812  5.881  19.276 4.683   -2.107 -0.398 C05 YMY 9  
YMY C09 C10 C 0 1 N N N N N N 5.819  6.044  20.194 6.098   -1.952 0.206  C09 YMY 10 
YMY C12 C11 C 0 1 N N N N N N 8.919  4.436  21.768 1.915   0.119  0.024  C12 YMY 11 
YMY C19 C12 C 0 1 N N N N N N 9.890  7.413  21.962 -1.645  0.422  0.797  C19 YMY 12 
YMY C23 C13 C 0 1 N N N N N N 9.068  12.190 22.010 -5.435  -0.988 -0.260 C23 YMY 13 
YMY C25 C14 C 0 1 N N N N N N 9.729  13.605 23.966 -7.884  -0.598 -0.562 C25 YMY 14 
YMY C06 C15 C 0 1 N N N N N N 6.469  6.814  18.021 4.759   -3.390 -1.196 C06 YMY 15 
YMY C08 C16 C 0 1 N N N N N N 5.111  7.406  19.860 6.594   -3.415 0.228  C08 YMY 16 
YMY C14 C17 C 0 1 N N N N N N 11.056 3.963  22.974 0.935   -1.016 1.998  C14 YMY 17 
YMY C16 C18 C 0 1 N N N N N N 13.353 4.890  22.222 -0.069  -2.146 3.988  C16 YMY 18 
YMY C17 C19 C 0 1 N N N N N N 13.121 3.503  24.372 0.018   0.349  3.879  C17 YMY 19 
YMY C26 C20 C 0 1 N N N N N N 10.470 14.900 24.406 -9.090  -0.867 -1.464 C26 YMY 20 
YMY C27 C21 C 0 1 N N N N N N 9.610  16.194 24.111 -10.355 -0.316 -0.802 C27 YMY 21 
YMY C28 C22 C 0 1 N N N N N N 10.232 17.471 24.792 -11.561 -0.584 -1.704 C28 YMY 22 
YMY C29 C23 C 0 1 N N N N N N 10.387 12.405 24.646 -7.658  0.911  -0.448 C29 YMY 23 
YMY C30 C24 C 0 1 N N N N N N 9.921  11.034 24.111 -6.452  1.179  0.454  C30 YMY 24 
YMY N07 N1  N 0 1 N N N N N N 5.486  7.698  18.375 5.840   -4.100 -0.829 N07 YMY 25 
YMY N11 N2  N 0 1 N N N N N N 8.739  3.956  20.413 3.179   0.261  0.470  N11 YMY 26 
YMY N18 N3  N 0 1 N N N N N N 10.181 6.218  22.764 -0.494  -0.040 0.270  N18 YMY 27 
YMY O02 O1  O 0 1 N N N N N N 7.931  1.259  20.658 5.126   1.634  -2.357 O02 YMY 28 
YMY O10 O2  O 0 1 N N N N N N 6.988  6.763  16.948 3.960   -3.729 -2.043 O10 YMY 29 
YMY O20 O3  O 0 1 N N N N N N 9.835  8.619  22.713 -2.802  0.266  0.127  O20 YMY 30 
YMY O31 O4  O 0 1 N N N N N N 9.730  7.386  20.782 -1.638  0.979  1.877  O31 YMY 31 
YMY O32 O5  O 0 1 N N N N N N 8.020  4.453  22.565 1.703   -0.016 -1.163 O32 YMY 32 
YMY H1  H1  H 0 1 N N N N N N 10.888 5.069  21.160 0.751   1.079  1.533  H1  YMY 33 
YMY H2  H2  H 0 1 N N N N N N 12.250 5.445  23.997 -1.138  -0.919 2.576  H2  YMY 34 
YMY H3  H3  H 0 1 N N N N N N 8.042  9.690  22.535 -3.895  1.862  0.908  H3  YMY 35 
YMY H4  H4  H 0 1 N N N N N N 9.050  9.625  21.050 -4.152  0.298  1.717  H4  YMY 36 
YMY H5  H5  H 0 1 N N N N N N 10.826 10.973 22.168 -5.021  0.935  -1.137 H5  YMY 37 
YMY H6  H6  H 0 1 N N N N N N 10.763 13.530 22.075 -6.453  -0.842 -2.153 H6  YMY 38 
YMY H7  H7  H 0 1 N N N N N N 9.165  14.350 22.023 -6.802  -2.332 -1.243 H7  YMY 39 
YMY S1  S1  S 0 1 N Y N N N N 8.334  1.908  18.762 4.001   3.078  -0.430 S1  YMY 40 
YMY H9  H9  H 0 1 N N N N N N 6.583  1.693  19.200 3.113   1.426  -1.940 H9  YMY 41 
YMY H10 H10 H 0 1 N N N N N N 6.736  3.514  20.793 5.222   0.493  0.059  H10 YMY 42 
YMY H11 H11 H 0 1 N N N N N N 5.975  4.014  18.486 3.400   -1.097 -1.802 H11 YMY 43 
YMY H12 H12 H 0 1 N N N N N N 7.673  4.328  17.989 5.139   -0.826 -2.069 H12 YMY 44 
YMY H13 H13 H 0 1 N N N N N N 7.781  6.209  19.682 3.938   -2.191 0.393  H13 YMY 45 
YMY H14 H14 H 0 1 N N N N N N 5.099  5.216  20.124 6.730   -1.336 -0.435 H14 YMY 46 
YMY H15 H15 H 0 1 N N N N N N 6.243  6.076  21.209 6.050   -1.540 1.214  H15 YMY 47 
YMY H16 H16 H 0 1 N N N N N N 8.027  12.175 22.364 -4.549  -1.458 -0.688 H16 YMY 48 
YMY H17 H17 H 0 1 N N N N N N 9.083  12.124 20.912 -5.623  -1.403 0.730  H17 YMY 49 
YMY H18 H18 H 0 1 N N N N N N 8.687  13.673 24.312 -8.072  -1.013 0.429  H18 YMY 50 
YMY H19 H19 H 0 1 N N N N N N 5.481  8.206  20.517 7.662   -3.455 0.016  H19 YMY 51 
YMY H20 H20 H 0 1 N N N N N N 4.021  7.314  19.973 6.385   -3.869 1.197  H20 YMY 52 
YMY H21 H21 H 0 1 N N N N N N 10.445 3.757  23.865 0.861   -1.969 1.474  H21 YMY 53 
YMY H22 H22 H 0 1 N N N N N N 11.215 3.029  22.414 1.911   -0.940 2.477  H22 YMY 54 
YMY H23 H23 H 0 1 N N N N N N 14.310 5.281  22.598 -0.851  -2.085 4.745  H23 YMY 55 
YMY H24 H24 H 0 1 N N N N N N 13.537 3.991  21.615 -0.197  -3.058 3.405  H24 YMY 56 
YMY H25 H25 H 0 1 N N N N N N 12.862 5.656  21.604 0.907   -2.159 4.473  H25 YMY 57 
YMY H26 H26 H 0 1 N N N N N N 12.446 3.267  25.208 -0.048  1.214  3.219  H26 YMY 58 
YMY H27 H27 H 0 1 N N N N N N 13.350 2.582  23.815 -0.763  0.409  4.636  H27 YMY 59 
YMY H28 H28 H 0 1 N N N N N N 14.053 3.936  24.764 0.994   0.336  4.364  H28 YMY 60 
YMY H29 H29 H 0 1 N N N N N N 10.673 14.845 25.486 -8.941  -0.376 -2.426 H29 YMY 61 
YMY H30 H30 H 0 1 N N N N N N 11.421 14.971 23.857 -9.198  -1.940 -1.617 H30 YMY 62 
YMY H31 H31 H 0 1 N N N N N N 9.568  16.354 23.024 -10.505 -0.807 0.160  H31 YMY 63 
YMY H32 H32 H 0 1 N N N N N N 8.592  16.042 24.499 -10.248 0.758  -0.649 H32 YMY 64 
YMY H33 H33 H 0 1 N N N N N N 9.609  18.348 24.565 -12.462 -0.192 -1.233 H33 YMY 65 
YMY H34 H34 H 0 1 N N N N N N 10.273 17.322 25.881 -11.412 -0.094 -2.666 H34 YMY 66 
YMY H35 H35 H 0 1 N N N N N N 11.249 17.634 24.405 -11.669 -1.658 -1.857 H35 YMY 67 
YMY H36 H36 H 0 1 N N N N N N 11.475 12.480 24.499 -7.470  1.325  -1.439 H36 YMY 68 
YMY H37 H37 H 0 1 N N N N N N 10.158 12.451 25.721 -8.544  1.380  -0.020 H37 YMY 69 
YMY H38 H38 H 0 1 N N N N N N 8.934  10.807 24.540 -6.640  0.764  1.445  H38 YMY 70 
YMY H39 H39 H 0 1 N N N N N N 10.644 10.269 24.430 -6.291  2.254  0.535  H39 YMY 71 
YMY H40 H40 H 0 1 N N N N N N 5.083  8.401  17.789 6.090   -4.954 -1.214 H40 YMY 72 
YMY H41 H41 H 0 1 N N N N N N 9.512  3.967  19.779 3.355   0.298  1.423  H41 YMY 73 
YMY H42 H42 H 0 1 N N N N N N 10.275 6.286  23.757 -0.499  -0.485 -0.592 H42 YMY 74 
YMY H43 H43 H 0 1 N N N N N N 8.019  0.344  20.420 5.215   0.851  -2.917 H43 YMY 75 
YMY O1  O6  O 0 1 N Y N N N N ?      ?      ?      5.128   3.159  0.431  O1  YMY 76 
YMY O2  O7  O 0 1 N Y N N N N ?      ?      ?      3.619   4.180  -1.242 O2  YMY 77 
YMY O3  O8  O 0 1 N Y N N N N ?      ?      ?      2.822   2.880  0.512  O3  YMY 78 
YMY H8  H8  H 0 1 N Y N N N N ?      ?      ?      2.665   3.625  1.108  H8  YMY 79 
# 
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 
YMY O10 C06 DOUB N N 1  
YMY C06 N07 SING N N 2  
YMY C06 C05 SING N N 3  
YMY N07 C08 SING N N 4  
YMY C04 C05 SING N N 5  
YMY C04 C03 SING N N 6  
YMY C05 C09 SING N N 7  
YMY C01 C03 SING N N 8  
YMY C01 O02 SING N N 9  
YMY C08 C09 SING N N 10 
YMY C03 N11 SING N N 11 
YMY N11 C12 SING N N 12 
YMY O31 C19 DOUB N N 13 
YMY C12 C13 SING N N 14 
YMY C12 O32 DOUB N N 15 
YMY C19 O20 SING N N 16 
YMY C19 N18 SING N N 17 
YMY C23 C24 SING N N 18 
YMY C23 C22 SING N N 19 
YMY C13 N18 SING N N 20 
YMY C13 C14 SING N N 21 
YMY C21 C22 SING N N 22 
YMY C21 O20 SING N N 23 
YMY C16 C15 SING N N 24 
YMY C24 C25 SING N N 25 
YMY C22 C30 SING N N 26 
YMY C14 C15 SING N N 27 
YMY C15 C17 SING N N 28 
YMY C25 C26 SING N N 29 
YMY C25 C29 SING N N 30 
YMY C30 C29 SING N N 31 
YMY C27 C26 SING N N 32 
YMY C27 C28 SING N N 33 
YMY C13 H1  SING N N 34 
YMY C15 H2  SING N N 35 
YMY C21 H3  SING N N 36 
YMY C21 H4  SING N N 37 
YMY C22 H5  SING N N 38 
YMY C24 H6  SING N N 39 
YMY C24 H7  SING N N 40 
YMY C01 S1  SING N N 41 
YMY C01 H9  SING N N 42 
YMY C03 H10 SING N N 43 
YMY C04 H11 SING N N 44 
YMY C04 H12 SING N N 45 
YMY C05 H13 SING N N 46 
YMY C09 H14 SING N N 47 
YMY C09 H15 SING N N 48 
YMY C23 H16 SING N N 49 
YMY C23 H17 SING N N 50 
YMY C25 H18 SING N N 51 
YMY C08 H19 SING N N 52 
YMY C08 H20 SING N N 53 
YMY C14 H21 SING N N 54 
YMY C14 H22 SING N N 55 
YMY C16 H23 SING N N 56 
YMY C16 H24 SING N N 57 
YMY C16 H25 SING N N 58 
YMY C17 H26 SING N N 59 
YMY C17 H27 SING N N 60 
YMY C17 H28 SING N N 61 
YMY C26 H29 SING N N 62 
YMY C26 H30 SING N N 63 
YMY C27 H31 SING N N 64 
YMY C27 H32 SING N N 65 
YMY C28 H33 SING N N 66 
YMY C28 H34 SING N N 67 
YMY C28 H35 SING N N 68 
YMY C29 H36 SING N N 69 
YMY C29 H37 SING N N 70 
YMY C30 H38 SING N N 71 
YMY C30 H39 SING N N 72 
YMY N07 H40 SING N N 73 
YMY N11 H41 SING N N 74 
YMY N18 H42 SING N N 75 
YMY O02 H43 SING N N 76 
YMY S1  O1  DOUB N N 77 
YMY S1  O2  DOUB N N 78 
YMY S1  O3  SING N N 79 
YMY O3  H8  SING N N 80 
# 
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 
YMY SMILES           ACDLabs              12.01 "CC(C)CC(NC(=O)OCC1CCC(CCC)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O"                                                                                                                                                                  
YMY InChI            InChI                1.03  "InChI=1S/C24H43N3O8S/c1-4-5-16-6-8-17(9-7-16)14-35-24(31)27-19(12-15(2)3)22(29)26-20(23(30)36(32,33)34)13-18-10-11-25-21(18)28/h15-20,23,30H,4-14H2,1-3H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t16-,17-,18-,19-,20-,23+/m0/s1" 
YMY InChIKey         InChI                1.03  ZJKUZJJPWZXFHP-LLQGSFPOSA-N                                                                                                                                                                                                        
YMY SMILES_CANONICAL CACTVS               3.385 "CCC[C@H]1CC[C@@H](CC1)COC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                    
YMY SMILES           CACTVS               3.385 "CCC[CH]1CC[CH](CC1)COC(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O"                                                                                                                                              
YMY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCC1CCC(CC1)COC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C(O)S(=O)(=O)O"                                                                                                                                                   
YMY SMILES           "OpenEye OEToolkits" 2.0.7 "CCCC1CCC(CC1)COC(=O)NC(CC(C)C)C(=O)NC(CC2CCNC2=O)C(O)S(=O)(=O)O"                                                                                                                                                                  
# 
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 
YMY "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1s,4S)-4-propylcyclohexyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid"                           
YMY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-4-methyl-2-[(4-propylcyclohexyl)methoxycarbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic 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 
YMY "Create component" 2021-03-12 RCSB 
YMY "Initial release"  2021-03-24 RCSB 
YMY "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YMY 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_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               C01 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
