data_YMD
# 
_chem_comp.id                                    YMD 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H39 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                        505.625 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMD 
_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        7LZX 
_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 
YMD C02 C1  C 0 1 N N N N N N 11.287 24.038 25.682 2.427  -0.130 0.014  C02 YMD 1  
YMD C04 C2  C 0 1 N N S N N N 12.281 22.070 26.913 0.072  0.081  0.600  C04 YMD 2  
YMD C05 C3  C 0 1 N N N N N N 13.388 21.813 27.926 -0.032 1.434  1.306  C05 YMD 3  
YMD C06 C4  C 0 1 N N N N N N 14.739 22.280 27.404 1.236  1.681  2.126  C06 YMD 4  
YMD C07 C5  C 0 1 N N N N N N 15.124 21.515 26.145 1.187  3.085  2.731  C07 YMD 5  
YMD C08 C6  C 0 1 N N N N N N 15.815 22.159 28.478 1.327  0.644  3.248  C08 YMD 6  
YMD C09 C7  C 0 1 N N N N N N 10.963 21.576 27.482 -1.225 -0.217 -0.108 C09 YMD 7  
YMD C11 C8  C 0 1 N N S N N N 9.119  19.881 27.404 -3.647 -0.484 -0.103 C11 YMD 8  
YMD C12 C9  C 0 1 N N N N N N 8.018  19.892 26.309 -3.852 0.663  -1.096 C12 YMD 9  
YMD C13 C10 C 0 1 N N S N N N 7.750  21.185 25.694 -3.955 1.985  -0.333 C13 YMD 10 
YMD C14 C11 C 0 1 N N N N N N 6.699  21.026 24.503 -4.149 3.137  -1.294 C14 YMD 11 
YMD C16 C12 C 0 1 N N N N N N 6.034  22.712 26.034 -5.667 3.482  0.429  C16 YMD 12 
YMD C17 C13 C 0 1 N N N N N N 7.049  22.065 26.699 -5.228 2.005  0.544  C17 YMD 13 
YMD C19 C14 C 0 1 N N R N N N 9.303  18.502 28.036 -3.632 -1.815 -0.858 C19 YMD 14 
YMD C23 C15 C 0 1 N N N N N N 10.288 25.925 24.700 4.766  -0.380 -0.392 C23 YMD 15 
YMD C24 C16 C 0 1 N N N N N N 8.883  26.063 25.279 5.594  -1.023 -1.506 C24 YMD 16 
YMD C25 C17 C 0 1 N N N N N N 7.947  26.802 24.330 7.003  -1.320 -0.988 C25 YMD 17 
YMD C26 C18 C 0 1 N N N N N N 8.507  28.155 23.900 7.669  -0.016 -0.544 C26 YMD 18 
YMD C27 C19 C 0 1 N N N N N N 7.596  28.724 22.822 9.077  -0.313 -0.026 C27 YMD 19 
YMD C28 C20 C 0 1 N N N N N N 8.495  29.123 25.083 7.755  0.943  -1.734 C28 YMD 20 
YMD C29 C21 C 0 1 N N N N N N 9.920  28.042 23.340 6.840  0.627  0.570  C29 YMD 21 
YMD C30 C22 C 0 1 N N N N N N 10.856 27.275 24.268 5.432  0.925  0.051  C30 YMD 22 
YMD N03 N1  N 0 1 N N N N N N 12.194 23.488 26.657 1.163  0.123  -0.377 N03 YMD 23 
YMD N10 N2  N 0 1 N N N N N N 10.376 20.398 26.897 -2.372 -0.304 0.595  N10 YMD 24 
YMD N15 N3  N 0 1 N N N N N N 5.714  21.911 24.713 -5.115 3.956  -0.846 N15 YMD 25 
YMD O01 O1  O 0 1 N N N N N N 10.698 23.350 24.925 2.663  -0.392 1.177  O01 YMD 26 
YMD O18 O2  O 0 1 N N N N N N 6.771  20.287 23.601 -3.522 3.298  -2.320 O18 YMD 27 
YMD O20 O3  O 0 1 N N N N N N 10.126 18.679 29.160 -4.868 -1.982 -1.555 O20 YMD 28 
YMD O21 O4  O 0 1 N N N N N N 10.422 22.151 28.361 -1.237 -0.379 -1.310 O21 YMD 29 
YMD O22 O5  O 0 1 N N N N N N 11.136 25.421 25.674 3.429  -0.097 -0.885 O22 YMD 30 
YMD H1  H1  H 0 1 N N N N N N 12.504 21.525 25.984 0.272  -0.698 1.335  H1  YMD 31 
YMD H2  H2  H 0 1 N N N N N N 13.156 22.355 28.854 -0.144 2.224  0.563  H2  YMD 32 
YMD H3  H3  H 0 1 N N N N N N 13.439 20.734 28.135 -0.899 1.433  1.968  H3  YMD 33 
YMD H4  H4  H 0 1 N N N N N N 14.648 23.343 27.137 2.109  1.594  1.479  H4  YMD 34 
YMD H5  H5  H 0 1 N N N N N N 16.102 21.868 25.786 0.314  3.172  3.378  H5  YMD 35 
YMD H6  H6  H 0 1 N N N N N N 15.183 20.440 26.373 2.091  3.260  3.315  H6  YMD 36 
YMD H7  H7  H 0 1 N N N N N N 14.365 21.684 25.367 1.122  3.823  1.932  H7  YMD 37 
YMD H8  H8  H 0 1 N N N N N N 15.507 22.721 29.372 2.230  0.820  3.832  H8  YMD 38 
YMD H9  H9  H 0 1 N N N N N N 15.953 21.100 28.741 0.454  0.731  3.894  H9  YMD 39 
YMD H10 H10 H 0 1 N N N N N N 16.762 22.568 28.096 1.361  -0.356 2.817  H10 YMD 40 
YMD H11 H11 H 0 1 N N N N N N 8.775  20.555 28.202 -4.461 -0.486 0.622  H11 YMD 41 
YMD H12 H12 H 0 1 N N N N N N 7.083  19.535 26.766 -3.006 0.704  -1.782 H12 YMD 42 
YMD H13 H13 H 0 1 N N N N N N 8.326  19.197 25.514 -4.769 0.495  -1.660 H13 YMD 43 
YMD H14 H14 H 0 1 N N N N N N 8.669  21.662 25.322 -3.067 2.141  0.279  H14 YMD 44 
YMD H15 H15 H 0 1 N N N N N N 6.349  23.735 25.781 -6.754 3.553  0.420  H15 YMD 45 
YMD H16 H16 H 0 1 N N N N N N 5.138  22.751 26.671 -5.258 4.062  1.257  H16 YMD 46 
YMD H17 H17 H 0 1 N N N N N N 6.635  21.452 27.513 -5.991 1.340  0.140  H17 YMD 47 
YMD H18 H18 H 0 1 N N N N N N 7.755  22.799 27.115 -4.995 1.747  1.577  H18 YMD 48 
YMD S1  S1  S 0 1 N Y N N N N 9.751  17.823 27.341 -3.414 -3.176 0.322  S1  YMD 49 
YMD H20 H20 H 0 1 N N N N N N 8.310  18.186 28.389 -2.809 -1.818 -1.572 H20 YMD 50 
YMD H21 H21 H 0 1 N N N N N N 10.251 25.257 23.827 4.704  -1.062 0.455  H21 YMD 51 
YMD H22 H22 H 0 1 N N N N N N 8.942  26.620 26.226 5.120  -1.952 -1.822 H22 YMD 52 
YMD H23 H23 H 0 1 N N N N N N 8.476  25.059 25.469 5.656  -0.340 -2.354 H23 YMD 53 
YMD H24 H24 H 0 1 N N N N N N 6.984  26.963 24.837 6.941  -2.003 -0.140 H24 YMD 54 
YMD H25 H25 H 0 1 N N N N N N 7.791  26.183 23.434 7.593  -1.778 -1.781 H25 YMD 55 
YMD H26 H26 H 0 1 N N N N N N 6.572  28.810 23.215 9.667  -0.771 -0.819 H26 YMD 56 
YMD H27 H27 H 0 1 N N N N N N 7.959  29.718 22.523 9.552  0.616  0.290  H27 YMD 57 
YMD H28 H28 H 0 1 N N N N N N 7.599  28.055 21.949 9.016  -0.996 0.822  H28 YMD 58 
YMD H29 H29 H 0 1 N N N N N N 9.147  28.737 25.880 6.752  1.155  -2.103 H29 YMD 59 
YMD H30 H30 H 0 1 N N N N N N 8.861  30.107 24.755 8.230  1.872  -1.418 H30 YMD 60 
YMD H31 H31 H 0 1 N N N N N N 7.468  29.222 25.465 8.345  0.485  -2.527 H31 YMD 61 
YMD H32 H32 H 0 1 N N N N N N 9.876  27.519 22.373 6.779  -0.055 1.417  H32 YMD 62 
YMD H33 H33 H 0 1 N N N N N N 10.323 29.055 23.191 7.315  1.556  0.885  H33 YMD 63 
YMD H34 H34 H 0 1 N N N N N N 11.808 27.104 23.744 5.493  1.607  -0.797 H34 YMD 64 
YMD H35 H35 H 0 1 N N N N N N 11.036 27.884 25.166 4.842  1.383  0.844  H35 YMD 65 
YMD H36 H36 H 0 1 N N N N N N 12.783 24.109 27.174 0.975  0.332  -1.305 H36 YMD 66 
YMD H37 H37 H 0 1 N N N N N N 10.836 19.935 26.139 -2.353 -0.247 1.563  H37 YMD 67 
YMD H38 H38 H 0 1 N N N N N N 4.912  22.041 24.130 -5.411 4.757  -1.306 H38 YMD 68 
YMD H39 H39 H 0 1 N N N N N N 10.267 17.841 29.585 -5.051 -1.288 -2.204 H39 YMD 69 
YMD O1  O6  O 0 1 N Y N N N N ?      ?      ?      -4.342 -3.062 1.392  O1  YMD 70 
YMD O2  O7  O 0 1 N Y N N N N ?      ?      ?      -3.236 -4.407 -0.365 O2  YMD 71 
YMD O3  O8  O 0 1 N Y N N N N ?      ?      ?      -2.062 -2.907 0.967  O3  YMD 72 
YMD H19 H19 H 0 1 N Y N N N N ?      ?      ?      -1.806 -3.562 1.630  H19 YMD 73 
# 
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 
YMD C27 C26 SING N N 1  
YMD C29 C26 SING N N 2  
YMD C29 C30 SING N N 3  
YMD O18 C14 DOUB N N 4  
YMD C26 C25 SING N N 5  
YMD C26 C28 SING N N 6  
YMD C30 C23 SING N N 7  
YMD C25 C24 SING N N 8  
YMD C14 N15 SING N N 9  
YMD C14 C13 SING N N 10 
YMD C23 C24 SING N N 11 
YMD C23 O22 SING N N 12 
YMD N15 C16 SING N N 13 
YMD O01 C02 DOUB N N 14 
YMD O22 C02 SING N N 15 
YMD C02 N03 SING N N 16 
YMD C13 C12 SING N N 17 
YMD C13 C17 SING N N 18 
YMD C16 C17 SING N N 19 
YMD C07 C06 SING N N 20 
YMD C12 C11 SING N N 21 
YMD N03 C04 SING N N 22 
YMD N10 C11 SING N N 23 
YMD N10 C09 SING N N 24 
YMD C04 C09 SING N N 25 
YMD C04 C05 SING N N 26 
YMD C11 C19 SING N N 27 
YMD C06 C05 SING N N 28 
YMD C06 C08 SING N N 29 
YMD C09 O21 DOUB N N 30 
YMD C19 O20 SING N N 31 
YMD C04 H1  SING N N 32 
YMD C05 H2  SING N N 33 
YMD C05 H3  SING N N 34 
YMD C06 H4  SING N N 35 
YMD C07 H5  SING N N 36 
YMD C07 H6  SING N N 37 
YMD C07 H7  SING N N 38 
YMD C08 H8  SING N N 39 
YMD C08 H9  SING N N 40 
YMD C08 H10 SING N N 41 
YMD C11 H11 SING N N 42 
YMD C12 H12 SING N N 43 
YMD C12 H13 SING N N 44 
YMD C13 H14 SING N N 45 
YMD C16 H15 SING N N 46 
YMD C16 H16 SING N N 47 
YMD C17 H17 SING N N 48 
YMD C17 H18 SING N N 49 
YMD C19 S1  SING N N 50 
YMD C19 H20 SING N N 51 
YMD C23 H21 SING N N 52 
YMD C24 H22 SING N N 53 
YMD C24 H23 SING N N 54 
YMD C25 H24 SING N N 55 
YMD C25 H25 SING N N 56 
YMD C27 H26 SING N N 57 
YMD C27 H27 SING N N 58 
YMD C27 H28 SING N N 59 
YMD C28 H29 SING N N 60 
YMD C28 H30 SING N N 61 
YMD C28 H31 SING N N 62 
YMD C29 H32 SING N N 63 
YMD C29 H33 SING N N 64 
YMD C30 H34 SING N N 65 
YMD C30 H35 SING N N 66 
YMD N03 H36 SING N N 67 
YMD N10 H37 SING N N 68 
YMD N15 H38 SING N N 69 
YMD O20 H39 SING N N 70 
YMD S1  O1  DOUB N N 71 
YMD S1  O2  DOUB N N 72 
YMD S1  O3  SING N N 73 
YMD O3  H19 SING N N 74 
# 
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 
YMD SMILES           ACDLabs              12.01 "CC(C)CC(NC(=O)OC1CCC(C)(C)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O"                                                                                                                                                    
YMD InChI            InChI                1.03  "InChI=1S/C22H39N3O8S/c1-13(2)11-16(25-21(29)33-15-5-8-22(3,4)9-6-15)19(27)24-17(20(28)34(30,31)32)12-14-7-10-23-18(14)26/h13-17,20,28H,5-12H2,1-4H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t14-,16-,17-,20+/m0/s1" 
YMD InChIKey         InChI                1.03  LGCFVMZACNBZBJ-JWWIWJDOSA-N                                                                                                                                                                                          
YMD SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                
YMD SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O"                                                                                                                                      
YMD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)(C)C"                                                                                                                                     
YMD SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)(C)C"                                                                                                                                                    
# 
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 
YMD "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2S)-2-[(N-{[(4,4-dimethylcyclohexyl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid"                                    
YMD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-2-[(4,4-dimethylcyclohexyl)oxycarbonylamino]-4-methyl-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 
YMD "Create component" 2021-03-12 RCSB 
YMD "Initial release"  2021-03-24 RCSB 
YMD "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YMD 
_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               C19 
_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      ? 
# 
