data_Y8Y
# 
_chem_comp.id                                    Y8Y 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-(((((1R,3r,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)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                               "C24 H41 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                     2021-02-10 
_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                        531.663 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y8Y 
_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        7LKR 
_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 
Y8Y N11 N1  N 0 1 N N N N N N -18.801 -5.735 4.871  -2.651 -0.266 0.556  N11 Y8Y 1  
Y8Y C12 C1  C 0 1 N N N N N N -19.563 -6.103 3.769  -1.465 0.103  0.031  C12 Y8Y 2  
Y8Y C14 C2  C 0 1 N N N N N N -21.834 -7.296 4.072  -0.699 2.093  1.296  C14 Y8Y 3  
Y8Y C15 C3  C 0 1 N N N N N N -23.384 -7.198 4.098  -2.007 2.142  2.089  C15 Y8Y 4  
Y8Y C16 C4  C 0 1 N N N N N N -23.877 -5.936 4.825  -1.813 1.443  3.436  C16 Y8Y 5  
Y8Y O20 O1  O 0 1 N N N N N N -21.146 -4.102 0.481  3.221  0.314  0.277  O20 Y8Y 6  
Y8Y C23 C5  C 0 1 N N N N N N -21.288 -3.405 -2.719 6.860  -0.229 1.066  C23 Y8Y 7  
Y8Y C24 C6  C 0 1 N N S N N N -22.140 -3.064 -3.965 8.177  -0.101 0.313  C24 Y8Y 8  
Y8Y C25 C7  C 0 1 N N N N N N -22.110 -1.584 -4.263 8.267  1.270  -0.356 C25 Y8Y 9  
Y8Y C26 C8  C 0 1 N N R N N N -22.521 -0.808 -3.034 7.129  1.378  -1.371 C26 Y8Y 10 
Y8Y C27 C9  C 0 1 N N N N N N -21.617 -1.106 -1.817 5.783  1.272  -0.672 C27 Y8Y 11 
Y8Y C28 C10 C 0 1 N N N N N N -23.986 -1.150 -2.708 7.298  0.320  -2.453 C28 Y8Y 12 
Y8Y C29 C11 C 0 1 N N N N N N -24.349 -2.654 -2.757 7.380  -1.089 -1.885 C29 Y8Y 13 
Y8Y C02 C12 C 0 1 N N N N N N -16.239 -2.240 3.702  -5.121 2.306  -1.867 C02 Y8Y 14 
Y8Y C04 C13 C 0 1 N N N N N N -15.132 -3.241 1.885  -6.918 2.193  -0.399 C04 Y8Y 15 
Y8Y C05 C14 C 0 1 N N N N N N -16.178 -4.261 2.474  -6.047 0.953  -0.095 C05 Y8Y 16 
Y8Y C06 C15 C 0 1 N N S N N N -16.847 -3.642 3.702  -4.715 1.326  -0.788 C06 Y8Y 17 
Y8Y C07 C16 C 0 1 N N N N N N -16.569 -4.512 4.985  -4.068 0.086  -1.407 C07 Y8Y 18 
Y8Y C08 C17 C 0 1 N N S N N N -17.353 -5.867 5.009  -3.667 -0.888 -0.297 C08 Y8Y 19 
Y8Y C09 C18 C 0 1 N N R N N N -17.021 -6.624 6.319  -3.099 -2.165 -0.919 C09 Y8Y 20 
Y8Y C13 C19 C 0 1 N N S N N N -21.126 -5.929 3.727  -0.380 0.643  0.927  C13 Y8Y 21 
Y8Y C17 C20 C 0 1 N N N N N N -24.074 -8.452 4.673  -2.407 3.600  2.324  C17 Y8Y 22 
Y8Y C19 C21 C 0 1 N N N N N N -21.017 -4.296 1.834  2.050  0.470  0.924  C19 Y8Y 23 
Y8Y C21 C22 C 0 1 N N N N N N -20.707 -2.969 -0.204 4.414  0.192  1.095  C21 Y8Y 24 
Y8Y C22 C23 C 0 1 N N R N N N -21.620 -2.612 -1.420 5.647  0.021  0.183  C22 Y8Y 25 
Y8Y C30 C24 C 0 1 N N N N N N -23.585 -3.513 -3.761 8.349  -1.205 -0.720 C30 Y8Y 26 
Y8Y N03 N2  N 0 1 N N N N N N -15.306 -2.021 2.681  -6.358 2.774  -1.626 N03 Y8Y 27 
Y8Y N18 N3  N 0 1 N N N N N N -21.590 -5.432 2.420  0.904  0.590  0.225  N18 Y8Y 28 
Y8Y O01 O2  O 0 1 N N N N N N -16.533 -1.347 4.492  -4.428 2.627  -2.809 O01 Y8Y 29 
Y8Y O10 O3  O 0 1 N N N N N N -17.585 -7.906 6.234  -4.076 -2.750 -1.781 O10 Y8Y 30 
Y8Y O31 O4  O 0 1 N N N N N N -20.398 -3.485 2.504  2.027  0.504  2.138  O31 Y8Y 31 
Y8Y O32 O5  O 0 1 N N N N N N -19.006 -6.574 2.774  -1.271 0.000  -1.162 O32 Y8Y 32 
Y8Y H1  H1  H 0 1 N N N N N N -19.293 -5.340 5.647  -2.829 -0.123 1.498  H1  Y8Y 33 
Y8Y H2  H2  H 0 1 N N N N N N -21.544 -8.040 3.315  -0.803 2.686  0.387  H2  Y8Y 34 
Y8Y H3  H3  H 0 1 N N N N N N -21.489 -7.627 5.062  0.109  2.500  1.904  H3  Y8Y 35 
Y8Y H4  H4  H 0 1 N N N N N N -23.711 -7.109 3.051  -2.792 1.636  1.527  H4  Y8Y 36 
Y8Y H5  H5  H 0 1 N N N N N N -24.977 -5.913 4.816  -1.483 0.417  3.269  H5  Y8Y 37 
Y8Y H6  H6  H 0 1 N N N N N N -23.519 -5.949 5.865  -1.061 1.976  4.017  H6  Y8Y 38 
Y8Y H7  H7  H 0 1 N N N N N N -23.488 -5.043 4.314  -2.757 1.437  3.982  H7  Y8Y 39 
Y8Y H8  H8  H 0 1 N N N N N N -21.423 -4.475 -2.503 6.790  -1.236 1.496  H8  Y8Y 40 
Y8Y H9  H9  H 0 1 N N N N N N -20.235 -3.212 -2.970 6.853  0.486  1.898  H9  Y8Y 41 
Y8Y H10 H10 H 0 1 N N N N N N -21.724 -3.607 -4.827 9.001  -0.177 1.041  H10 Y8Y 42 
Y8Y H11 H11 H 0 1 N N N N N N -21.091 -1.291 -4.557 8.165  2.052  0.395  H11 Y8Y 43 
Y8Y H12 H12 H 0 1 N N N N N N -22.807 -1.362 -5.085 9.224  1.369  -0.865 H12 Y8Y 44 
Y8Y H13 H13 H 0 1 N N N N N N -22.457 0.267  -3.257 7.195  2.371  -1.847 H13 Y8Y 45 
Y8Y H14 H14 H 0 1 N N N N N N -20.587 -0.809 -2.063 5.637  2.156  -0.038 H14 Y8Y 46 
Y8Y H15 H15 H 0 1 N N N N N N -21.974 -0.516 -0.960 4.986  1.277  -1.427 H15 Y8Y 47 
Y8Y H16 H16 H 0 1 N N N N N N -24.202 -0.783 -1.694 6.453  0.380  -3.148 H16 Y8Y 48 
Y8Y H17 H17 H 0 1 N N N N N N -24.625 -0.624 -3.432 8.211  0.533  -3.022 H17 Y8Y 49 
Y8Y H18 H18 H 0 1 N N N N N N -25.419 -2.730 -3.000 6.396  -1.459 -1.616 H18 Y8Y 50 
Y8Y H19 H19 H 0 1 N N N N N N -24.169 -3.073 -1.756 7.743  -1.755 -2.693 H19 Y8Y 51 
Y8Y H20 H20 H 0 1 N N N N N N -14.109 -3.630 1.992  -7.953 1.896  -0.562 H20 Y8Y 52 
Y8Y H21 H21 H 0 1 N N N N N N -16.941 -4.486 1.714  -5.907 0.828  0.979  H21 Y8Y 53 
Y8Y H22 H22 H 0 1 N N N N N N -15.664 -5.189 2.764  -6.478 0.055  -0.537 H22 Y8Y 54 
Y8Y H23 H23 H 0 1 N N N N N N -17.933 -3.576 3.539  -4.036 1.799  -0.079 H23 Y8Y 55 
Y8Y H24 H24 H 0 1 N N N N N N -15.492 -4.733 5.028  -4.778 -0.399 -2.076 H24 Y8Y 56 
Y8Y H25 H25 H 0 1 N N N N N N -16.859 -3.927 5.870  -3.181 0.381  -1.968 H25 Y8Y 57 
Y8Y H26 H26 H 0 1 N N N N N N -16.977 -6.475 4.173  -4.543 -1.135 0.304  H26 Y8Y 58 
Y8Y S1  S1  S 0 1 N Y N N N N -17.411 -6.098 7.165  -2.670 -3.339 0.395  S1  Y8Y 59 
Y8Y H28 H28 H 0 1 N N N N N N -15.927 -6.738 6.336  -2.205 -1.922 -1.494 H28 Y8Y 60 
Y8Y H29 H29 H 0 1 N N N N N N -21.404 -5.203 4.505  -0.324 0.041  1.833  H29 Y8Y 61 
Y8Y H30 H30 H 0 1 N N N N N N -25.165 -8.310 4.659  -2.546 4.098  1.364  H30 Y8Y 62 
Y8Y H31 H31 H 0 1 N N N N N N -23.811 -9.328 4.062  -3.339 3.634  2.889  H31 Y8Y 63 
Y8Y H32 H32 H 0 1 N N N N N N -23.738 -8.613 5.708  -1.623 4.106  2.886  H32 Y8Y 64 
Y8Y H33 H33 H 0 1 N N N N N N -19.687 -3.153 -0.571 4.533  1.090  1.701  H33 Y8Y 65 
Y8Y H34 H34 H 0 1 N N N N N N -20.698 -2.117 0.492  4.321  -0.677 1.746  H34 Y8Y 66 
Y8Y H35 H35 H 0 1 N N N N N N -22.651 -2.871 -1.137 5.454  -0.848 -0.446 H35 Y8Y 67 
Y8Y H36 H36 H 0 1 N N N N N N -24.105 -3.465 -4.729 9.377  -1.177 -1.104 H36 Y8Y 68 
Y8Y H37 H37 H 0 1 N N N N N N -23.580 -4.552 -3.399 8.210  -2.178 -0.232 H37 Y8Y 69 
Y8Y H38 H38 H 0 1 N N N N N N -22.326 -5.913 1.944  0.930  0.640  -0.744 H38 Y8Y 70 
Y8Y H39 H39 H 0 1 N N N N N N -17.394 -8.390 7.029  -4.352 -2.177 -2.509 H39 Y8Y 71 
Y8Y O1  O6  O 0 1 N Y N N N N ?       ?      ?      -3.778 -3.543 1.263  O1  Y8Y 72 
Y8Y O2  O7  O 0 1 N Y N N N N ?       ?      ?      -1.944 -4.439 -0.136 O2  Y8Y 73 
Y8Y O3  O8  O 0 1 N Y N N N N ?       ?      ?      -1.654 -2.598 1.252  O3  Y8Y 74 
Y8Y H27 H27 H 0 1 N N N N N N -15.340 -3.043 0.823  -6.854 2.909  0.420  H27 Y8Y 75 
Y8Y H40 H40 H 0 1 N N N N N N -14.828 -1.158 2.518  -6.822 3.411  -2.191 H40 Y8Y 76 
Y8Y H41 H41 H 0 1 N Y N N N N ?       ?      ?      -1.328 -3.108 2.006  H41 Y8Y 77 
# 
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 
Y8Y C25 C24 SING N N 1  
Y8Y C25 C26 SING N N 2  
Y8Y C24 C30 SING N N 3  
Y8Y C24 C23 SING N N 4  
Y8Y C30 C29 SING N N 5  
Y8Y C26 C28 SING N N 6  
Y8Y C26 C27 SING N N 7  
Y8Y C29 C28 SING N N 8  
Y8Y C23 C22 SING N N 9  
Y8Y C27 C22 SING N N 10 
Y8Y C22 C21 SING N N 11 
Y8Y C21 O20 SING N N 12 
Y8Y O20 C19 SING N N 13 
Y8Y C19 N18 SING N N 14 
Y8Y C19 O31 DOUB N N 15 
Y8Y C04 C05 SING N N 16 
Y8Y C04 N03 SING N N 17 
Y8Y N18 C13 SING N N 18 
Y8Y C05 C06 SING N N 19 
Y8Y N03 C02 SING N N 20 
Y8Y O32 C12 DOUB N N 21 
Y8Y C06 C02 SING N N 22 
Y8Y C06 C07 SING N N 23 
Y8Y C02 O01 DOUB N N 24 
Y8Y C13 C12 SING N N 25 
Y8Y C13 C14 SING N N 26 
Y8Y C12 N11 SING N N 27 
Y8Y C14 C15 SING N N 28 
Y8Y C15 C17 SING N N 29 
Y8Y C15 C16 SING N N 30 
Y8Y N11 C08 SING N N 31 
Y8Y C07 C08 SING N N 32 
Y8Y C08 C09 SING N N 33 
Y8Y O10 C09 SING N N 34 
Y8Y N11 H1  SING N N 35 
Y8Y C14 H2  SING N N 36 
Y8Y C14 H3  SING N N 37 
Y8Y C15 H4  SING N N 38 
Y8Y C16 H5  SING N N 39 
Y8Y C16 H6  SING N N 40 
Y8Y C16 H7  SING N N 41 
Y8Y C23 H8  SING N N 42 
Y8Y C23 H9  SING N N 43 
Y8Y C24 H10 SING N N 44 
Y8Y C25 H11 SING N N 45 
Y8Y C25 H12 SING N N 46 
Y8Y C26 H13 SING N N 47 
Y8Y C27 H14 SING N N 48 
Y8Y C27 H15 SING N N 49 
Y8Y C28 H16 SING N N 50 
Y8Y C28 H17 SING N N 51 
Y8Y C29 H18 SING N N 52 
Y8Y C29 H19 SING N N 53 
Y8Y C04 H20 SING N N 54 
Y8Y C05 H21 SING N N 55 
Y8Y C05 H22 SING N N 56 
Y8Y C06 H23 SING N N 57 
Y8Y C07 H24 SING N N 58 
Y8Y C07 H25 SING N N 59 
Y8Y C08 H26 SING N N 60 
Y8Y C09 S1  SING N N 61 
Y8Y C09 H28 SING N N 62 
Y8Y C13 H29 SING N N 63 
Y8Y C17 H30 SING N N 64 
Y8Y C17 H31 SING N N 65 
Y8Y C17 H32 SING N N 66 
Y8Y C21 H33 SING N N 67 
Y8Y C21 H34 SING N N 68 
Y8Y C22 H35 SING N N 69 
Y8Y C30 H36 SING N N 70 
Y8Y C30 H37 SING N N 71 
Y8Y N18 H38 SING N N 72 
Y8Y O10 H39 SING N N 73 
Y8Y S1  O1  DOUB N N 74 
Y8Y S1  O2  DOUB N N 75 
Y8Y S1  O3  SING N N 76 
Y8Y C04 H27 SING N N 77 
Y8Y N03 H40 SING N N 78 
Y8Y O3  H41 SING N N 79 
# 
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 
Y8Y InChI            InChI                1.03  "InChI=1S/C24H41N3O8S/c1-14(2)8-19(27-24(31)35-13-17-10-15-4-3-5-16(9-15)11-17)22(29)26-20(23(30)36(32,33)34)12-18-6-7-25-21(18)28/h14-20,23,30H,3-13H2,1-2H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t15-,16+,17+,18-,19-,20-,23+/m0/s1" 
Y8Y InChIKey         InChI                1.03  PGYROSRJIVXTOE-REFFYEJJSA-N                                                                                                                                                                                                               
Y8Y SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OC[C@H]1C[C@@H]2CCC[C@@H](C2)C1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                     
Y8Y SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OC[CH]1C[CH]2CCC[CH](C2)C1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O"                                                                                                                                                
Y8Y 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)OCC2C[C@@H]3CCC[C@@H](C3)C2"                                                                                                                                              
Y8Y SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CC3CCCC(C3)C2"                                                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           Y8Y 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-[[(2~{S})-2-[[(1~{R},5~{S})-3-bicyclo[3.3.1]nonanyl]methoxycarbonylamino]-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 
Y8Y "Create component" 2021-02-10 RCSB 
Y8Y "Initial release"  2021-02-17 RCSB 
Y8Y "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y8Y 
_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               C09 
_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      ? 
# 
