data_YM1
# 
_chem_comp.id                                    YM1 
_chem_comp.name                                  "(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H24 F5 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                        573.488 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YM1 
_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        7M04 
_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 
YM1 C12 C1  C 0 1 N N N N N N -19.588 -5.979 3.584  -1.556 0.374  0.098  C12 YM1 1  
YM1 C13 C2  C 0 1 N N S N N N -21.096 -5.766 3.562  -0.427 0.608  1.069  C13 YM1 2  
YM1 C14 C3  C 0 1 N N N N N N -21.762 -7.115 3.924  -0.507 2.037  1.609  C14 YM1 3  
YM1 C15 C4  C 0 1 N N N N N N -23.321 -7.009 4.014  -1.834 2.229  2.347  C15 YM1 4  
YM1 C16 C5  C 0 1 N N N N N N -23.785 -5.864 4.988  -1.849 1.359  3.605  C16 YM1 5  
YM1 C17 C6  C 0 1 N N N N N N -23.942 -8.337 4.432  -1.990 3.699  2.741  C17 YM1 6  
YM1 C19 C7  C 0 1 N N N N N N -21.098 -4.062 1.730  1.962  0.132  1.097  C19 YM1 7  
YM1 C21 C8  C 0 1 N N N N N N -21.564 -2.409 0.127  4.307  -0.257 1.310  C21 YM1 8  
YM1 C01 C9  C 0 1 N N S N N N -17.160 -6.531 6.140  -4.394 1.467  -0.858 C01 YM1 9  
YM1 C03 C10 C 0 1 N N S N N N -17.416 -5.712 4.863  -3.924 0.086  -0.397 C03 YM1 10 
YM1 C04 C11 C 0 1 N N N N N N -16.635 -4.383 4.884  -5.082 -0.647 0.283  C04 YM1 11 
YM1 C05 C12 C 0 1 N N R N N N -16.861 -3.561 3.582  -4.625 -2.047 0.700  C05 YM1 12 
YM1 C06 C13 C 0 1 N N N N N N -16.227 -2.086 3.780  -5.714 -2.751 1.485  C06 YM1 13 
YM1 C08 C14 C 0 1 N N N N N N -15.086 -3.224 2.049  -5.282 -3.930 -0.392 C08 YM1 14 
YM1 C09 C15 C 0 1 N N N N N N -16.258 -4.152 2.525  -4.435 -2.929 -0.517 C09 YM1 15 
YM1 C22 C16 C 0 1 Y N N N N N -22.079 -2.212 -1.331 5.547  -0.302 0.453  C22 YM1 16 
YM1 C23 C17 C 0 1 Y N N N N N -23.147 -2.977 -1.779 6.291  0.847  0.253  C23 YM1 17 
YM1 C25 C18 C 0 1 Y N N N N N -23.620 -2.811 -3.081 7.431  0.806  -0.535 C25 YM1 18 
YM1 C27 C19 C 0 1 Y N N N N N -23.034 -1.874 -3.930 7.824  -0.386 -1.122 C27 YM1 19 
YM1 C29 C20 C 0 1 Y N N N N N -21.970 -1.102 -3.482 7.078  -1.536 -0.920 C29 YM1 20 
YM1 C31 C21 C 0 1 Y N N N N N -21.487 -1.265 -2.180 5.942  -1.495 -0.128 C31 YM1 21 
YM1 F24 F1  F 0 1 N N N N N N -23.739 -3.898 -0.967 5.907  2.009  0.825  F24 YM1 22 
YM1 F26 F2  F 0 1 N N N N N N -24.661 -3.569 -3.504 8.157  1.928  -0.732 F26 YM1 23 
YM1 F28 F3  F 0 1 N N N N N N -23.505 -1.718 -5.202 8.932  -0.426 -1.894 F28 YM1 24 
YM1 F30 F4  F 0 1 N N N N N N -21.395 -0.185 -4.314 7.461  -2.699 -1.492 F30 YM1 25 
YM1 F32 F5  F 0 1 N N N N N N -20.446 -0.498 -1.757 5.215  -2.616 0.070  F32 YM1 26 
YM1 N07 N1  N 0 1 N N N N N N -15.209 -1.905 2.892  -6.034 -3.844 0.765  N07 YM1 27 
YM1 N11 N2  N 0 1 N N N N N N -18.848 -5.509 4.784  -2.818 0.237  0.551  N11 YM1 28 
YM1 N18 N3  N 0 1 N N N N N N -21.553 -5.346 2.259  0.854  0.415  0.385  N18 YM1 29 
YM1 O02 O1  O 0 1 N N N N N N -15.776 -6.630 6.263  -3.282 2.201  -1.373 O02 YM1 30 
YM1 O10 O2  O 0 1 N N N N N N -16.582 -1.279 4.579  -6.196 -2.403 2.543  O10 YM1 31 
YM1 O20 O3  O 0 1 N N N N N N -21.214 -3.775 0.343  3.157  0.053  0.481  O20 YM1 32 
YM1 O33 O4  O 0 1 N N N N N N -20.645 -3.244 2.466  1.884  -0.054 2.295  O33 YM1 33 
YM1 O34 O5  O 0 1 N N N N N N -19.019 -6.511 2.679  -1.329 0.313  -1.092 O34 YM1 34 
YM1 H1  H1  H 0 1 N N N N N N -21.368 -5.019 4.322  -0.507 -0.098 1.895  H1  YM1 35 
YM1 H2  H2  H 0 1 N N N N N N -21.503 -7.855 3.152  0.319  2.212  2.297  H2  YM1 36 
YM1 H3  H3  H 0 1 N N N N N N -21.374 -7.450 4.898  -0.447 2.742  0.781  H3  YM1 37 
YM1 H4  H4  H 0 1 N N N N N N -23.695 -6.760 3.010  -2.658 1.939  1.695  H4  YM1 38 
YM1 H5  H5  H 0 1 N N N N N N -24.884 -5.830 5.017  -1.666 0.320  3.331  H5  YM1 39 
YM1 H6  H6  H 0 1 N N N N N N -23.398 -6.063 5.998  -1.070 1.697  4.290  H6  YM1 40 
YM1 H7  H7  H 0 1 N N N N N N -23.397 -4.899 4.630  -2.820 1.441  4.093  H7  YM1 41 
YM1 H8  H8  H 0 1 N N N N N N -25.035 -8.230 4.486  -1.979 4.319  1.845  H8  YM1 42 
YM1 H9  H9  H 0 1 N N N N N N -23.685 -9.110 3.693  -2.935 3.836  3.267  H9  YM1 43 
YM1 H10 H10 H 0 1 N N N N N N -23.553 -8.629 5.419  -1.166 3.990  3.394  H10 YM1 44 
YM1 H11 H11 H 0 1 N N N N N N -20.679 -1.777 0.289  4.161  -1.225 1.788  H11 YM1 45 
YM1 H12 H12 H 0 1 N N N N N N -22.355 -2.120 0.834  4.422  0.512  2.074  H12 YM1 46 
YM1 H13 H13 H 0 1 N N N N N N -17.555 -7.538 5.943  -4.825 2.004  -0.013 H13 YM1 47 
YM1 S1  S1  S 0 1 N Y N N N N -17.594 -6.060 6.997  -5.648 1.277  -2.155 S1  YM1 48 
YM1 H15 H15 H 0 1 N N N N N N -17.077 -6.301 3.998  -3.587 -0.489 -1.260 H15 YM1 49 
YM1 H16 H16 H 0 1 N N N N N N -15.562 -4.602 4.985  -5.396 -0.090 1.166  H16 YM1 50 
YM1 H17 H17 H 0 1 N N N N N N -16.970 -3.786 5.745  -5.918 -0.729 -0.411 H17 YM1 51 
YM1 H18 H18 H 0 1 N N N N N N -17.943 -3.447 3.420  -3.706 -1.991 1.283  H18 YM1 52 
YM1 H19 H19 H 0 1 N N N N N N -14.345 -3.447 1.295  -5.378 -4.728 -1.113 H19 YM1 53 
YM1 H20 H20 H 0 1 N N N N N N -16.535 -5.099 2.085  -3.741 -2.769 -1.328 H20 YM1 54 
YM1 H21 H21 H 0 1 N N N N N N -14.645 -1.085 2.795  -6.708 -4.490 1.026  H21 YM1 55 
YM1 H22 H22 H 0 1 N N N N N N -19.335 -5.056 5.531  -2.993 0.240  1.505  H22 YM1 56 
YM1 H23 H23 H 0 1 N N N N N N -22.171 -5.924 1.727  0.904  0.493  -0.581 H23 YM1 57 
YM1 H24 H24 H 0 1 N N N N N N -15.562 -7.130 7.042  -2.572 2.341  -0.732 H24 YM1 58 
YM1 O1  O6  O 0 1 N Y N N N N ?       ?      ?      -6.125 2.548  -2.577 O1  YM1 59 
YM1 O2  O7  O 0 1 N Y N N N N ?       ?      ?      -5.243 0.296  -3.100 O2  YM1 60 
YM1 O3  O8  O 0 1 N Y N N N N ?       ?      ?      -6.837 0.647  -1.445 O3  YM1 61 
YM1 H14 H14 H 0 1 N Y N N N N ?       ?      ?      -7.597 0.483  -2.020 H14 YM1 62 
# 
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 
YM1 F28 C27 SING N N 1  
YM1 F30 C29 SING N N 2  
YM1 C27 C29 DOUB Y N 3  
YM1 C27 C25 SING Y N 4  
YM1 F26 C25 SING N N 5  
YM1 C29 C31 SING Y N 6  
YM1 C25 C23 DOUB Y N 7  
YM1 C31 F32 SING N N 8  
YM1 C31 C22 DOUB Y N 9  
YM1 C23 C22 SING Y N 10 
YM1 C23 F24 SING N N 11 
YM1 C22 C21 SING N N 12 
YM1 C21 O20 SING N N 13 
YM1 O20 C19 SING N N 14 
YM1 C19 N18 SING N N 15 
YM1 C19 O33 DOUB N N 16 
YM1 C08 C09 DOUB N N 17 
YM1 C08 N07 SING N N 18 
YM1 N18 C13 SING N N 19 
YM1 C09 C05 SING N N 20 
YM1 O34 C12 DOUB N N 21 
YM1 N07 C06 SING N N 22 
YM1 C13 C12 SING N N 23 
YM1 C13 C14 SING N N 24 
YM1 C05 C06 SING N N 25 
YM1 C05 C04 SING N N 26 
YM1 C12 N11 SING N N 27 
YM1 C06 O10 DOUB N N 28 
YM1 C14 C15 SING N N 29 
YM1 C15 C17 SING N N 30 
YM1 C15 C16 SING N N 31 
YM1 N11 C03 SING N N 32 
YM1 C03 C04 SING N N 33 
YM1 C03 C01 SING N N 34 
YM1 C01 O02 SING N N 35 
YM1 C13 H1  SING N N 36 
YM1 C14 H2  SING N N 37 
YM1 C14 H3  SING N N 38 
YM1 C15 H4  SING N N 39 
YM1 C16 H5  SING N N 40 
YM1 C16 H6  SING N N 41 
YM1 C16 H7  SING N N 42 
YM1 C17 H8  SING N N 43 
YM1 C17 H9  SING N N 44 
YM1 C17 H10 SING N N 45 
YM1 C21 H11 SING N N 46 
YM1 C21 H12 SING N N 47 
YM1 C01 H13 SING N N 48 
YM1 C01 S1  SING N N 49 
YM1 C03 H15 SING N N 50 
YM1 C04 H16 SING N N 51 
YM1 C04 H17 SING N N 52 
YM1 C05 H18 SING N N 53 
YM1 C08 H19 SING N N 54 
YM1 C09 H20 SING N N 55 
YM1 N07 H21 SING N N 56 
YM1 N11 H22 SING N N 57 
YM1 N18 H23 SING N N 58 
YM1 O02 H24 SING N N 59 
YM1 S1  O1  DOUB N N 60 
YM1 S1  O2  DOUB N N 61 
YM1 S1  O3  SING N N 62 
YM1 O3  H14 SING N N 63 
# 
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 
YM1 SMILES           ACDLabs              12.01 "O=C1NC=CC1CC(NC(=O)C(CC(C)C)NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(O)S(=O)(=O)O"                                                                                                                                                              
YM1 InChI            InChI                1.03  "InChI=1S/C21H24F5N3O8S/c1-8(2)5-11(29-21(33)37-7-10-13(22)15(24)17(26)16(25)14(10)23)19(31)28-12(20(32)38(34,35)36)6-9-3-4-27-18(9)30/h3-4,8-9,11-12,20,32H,5-7H2,1-2H3,(H,27,30)(H,28,31)(H,29,33)(H,34,35,36)/t9-,11-,12-,20-/m0/s1" 
YM1 InChIKey         InChI                1.03  VNVWDEQECYLCMA-JJDHJZHUSA-N                                                                                                                                                                                                             
YM1 SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[C@@H](C[C@@H]2C=CNC2=O)[C@@H](O)[S](O)(=O)=O"                                                                                                                                         
YM1 SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[CH](C[CH]2C=CNC2=O)[CH](O)[S](O)(=O)=O"                                                                                                                                                
YM1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F"                                                                                                                                               
YM1 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F"                                                                                                                                                              
# 
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 
YM1 "SYSTEMATIC NAME" ACDLabs              12.01 "(1S,2S)-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]-2-[(N-{[(pentafluorophenyl)methoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid"                                                 
YM1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-4-methyl-2-[[2,3,4,5,6-pentakis(fluoranyl)phenyl]methoxycarbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-1,3-dihydropyrrol-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 
YM1 "Create component" 2021-03-12 RCSB 
YM1 "Initial release"  2021-03-24 RCSB 
YM1 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YM1 
_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      ? 
# 
