data_Y4D
# 
_chem_comp.id                                    Y4D 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-(((((1R,3s,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                     2021-02-03 
_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                     Y4D 
_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        7LKU 
_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 
Y4D N11 N1  N 0 1 N N N N N N 10.370 20.433 27.010 2.837  -0.115 0.473  N11 Y4D 1  
Y4D C12 C1  C 0 1 N N N N N N 10.833 21.720 27.258 1.542  0.050  0.806  C12 Y4D 2  
Y4D C14 C2  C 0 1 N N N N N N 13.305 21.998 27.787 0.661  0.741  -1.406 C14 Y4D 3  
Y4D C15 C3  C 0 1 N N N N N N 14.702 22.497 27.360 -0.357 0.403  -2.498 C15 Y4D 4  
Y4D C16 C4  C 0 1 N N N N N N 15.159 21.841 26.041 -0.242 1.421  -3.634 C16 Y4D 5  
Y4D O20 O1  O 0 1 N N N N N N 10.789 25.505 25.547 -3.149 -0.335 0.447  O20 Y4D 6  
Y4D C23 C5  C 0 1 N N N N N N 7.005  26.505 25.087 -6.732 -1.465 0.079  C23 Y4D 7  
Y4D C24 C6  C 0 1 N N R N N N 5.735  26.705 25.966 -8.025 -1.066 0.788  C24 Y4D 8  
Y4D C25 C7  C 0 1 N N N N N N 5.950  26.189 27.392 -7.734 0.014  1.831  C25 Y4D 9  
Y4D C26 C8  C 0 1 N N S N N N 7.152  26.893 28.027 -7.133 1.237  1.136  C26 Y4D 10 
Y4D C27 C9  C 0 1 N N N N N N 8.450  26.699 27.189 -5.835 0.847  0.429  C27 Y4D 11 
Y4D C28 C10 C 0 1 N N N N N N 6.798  28.388 28.206 -8.133 1.785  0.117  C28 Y4D 12 
Y4D C29 C11 C 0 1 N N N N N N 6.188  29.081 26.953 -8.459 0.712  -0.922 C29 Y4D 13 
Y4D C02 C12 C 0 1 N N N N N N 6.802  21.066 24.469 3.810  -2.575 0.146  C02 Y4D 14 
Y4D C04 C13 C 0 1 N N N N N N 5.799  22.735 25.773 5.876  -3.285 -0.643 C04 Y4D 15 
Y4D C05 C14 C 0 1 N N N N N N 6.962  22.071 26.598 6.072  -3.015 0.865  C05 Y4D 16 
Y4D C06 C15 C 0 1 N N S N N N 7.746  21.155 25.661 4.818  -2.175 1.201  C06 Y4D 17 
Y4D C07 C16 C 0 1 N N N N N N 8.030  19.784 26.378 5.132  -0.681 1.101  C07 Y4D 18 
Y4D C08 C17 C 0 1 N N S N N N 9.114  19.853 27.477 3.886  0.128  1.467  C08 Y4D 19 
Y4D C09 C18 C 0 1 N N R N N N 9.323  18.442 28.041 4.233  1.618  1.488  C09 Y4D 20 
Y4D C13 C19 C 0 1 N N S N N N 12.192 22.226 26.693 0.463  -0.200 -0.216 C13 Y4D 21 
Y4D C17 C20 C 0 1 N N N N N N 15.754 22.305 28.481 -0.077 -1.000 -3.040 C17 Y4D 22 
Y4D C19 C21 C 0 1 N N N N N N 11.041 24.135 25.579 -1.944 -0.562 -0.109 C19 Y4D 23 
Y4D C21 C22 C 0 1 N N N N N N 9.560  25.993 24.954 -4.285 -1.024 -0.140 C21 Y4D 24 
Y4D C22 C23 C 0 1 N N S N N N 8.233  25.937 25.852 -5.561 -0.645 0.619  C22 Y4D 25 
Y4D C30 C24 C 0 1 N N N N N N 5.306  28.191 26.029 -9.029 -0.527 -0.234 C30 Y4D 26 
Y4D N03 N2  N 0 1 N N N N N N 5.720  21.947 24.543 4.429  -3.200 -0.871 N03 Y4D 27 
Y4D N18 N3  N 0 1 N N N N N N 12.116 23.629 26.310 -0.849 0.046  0.388  N18 Y4D 28 
Y4D O01 O2  O 0 1 N N N N N N 6.942  20.303 23.517 2.617  -2.368 0.212  O01 Y4D 29 
Y4D O10 O3  O 0 1 N N N N N N 10.145 18.540 29.179 3.102  2.364  1.942  O10 Y4D 30 
Y4D O31 O4  O 0 1 N N N N N N 10.291 23.378 24.975 -1.844 -1.314 -1.058 O31 Y4D 31 
Y4D O32 O5  O 0 1 N N N N N N 10.164 22.523 27.933 1.244  0.399  1.929  O32 Y4D 32 
Y4D H1  H1  H 0 1 N N N N N N 10.957 19.844 26.455 3.075  -0.398 -0.424 H1  Y4D 33 
Y4D H2  H2  H 0 1 N N N N N N 13.009 22.533 28.701 1.670  0.620  -1.801 H2  Y4D 34 
Y4D H3  H3  H 0 1 N N N N N N 13.370 20.920 27.998 0.518  1.772  -1.083 H3  Y4D 35 
Y4D H4  H4  H 0 1 N N N N N N 14.619 23.578 27.175 -1.363 0.438  -2.079 H4  Y4D 36 
Y4D H5  H5  H 0 1 N N N N N N 16.155 22.219 25.769 0.763  1.387  -4.053 H5  Y4D 37 
Y4D H6  H6  H 0 1 N N N N N N 15.204 20.750 26.171 -0.968 1.181  -4.412 H6  Y4D 38 
Y4D H7  H7  H 0 1 N N N N N N 14.443 22.086 25.243 -0.442 2.421  -3.248 H7  Y4D 39 
Y4D H8  H8  H 0 1 N N N N N N 7.286  27.480 24.661 -6.538 -2.526 0.254  H8  Y4D 40 
Y4D H9  H9  H 0 1 N N N N N N 6.754  25.808 24.274 -6.832 -1.297 -0.993 H9  Y4D 41 
Y4D H10 H10 H 0 1 N N N N N N 4.914  26.131 25.511 -8.451 -1.940 1.284  H10 Y4D 42 
Y4D H11 H11 H 0 1 N N N N N N 5.051  26.391 27.992 -8.667 0.301  2.322  H11 Y4D 43 
Y4D H12 H12 H 0 1 N N N N N N 6.136  25.105 27.363 -7.041 -0.368 2.577  H12 Y4D 44 
Y4D H13 H13 H 0 1 N N N N N N 7.321  26.459 29.023 -6.921 2.007  1.882  H13 Y4D 45 
Y4D H14 H14 H 0 1 N N N N N N 9.172  26.133 27.796 -5.914 1.072  -0.634 H14 Y4D 46 
Y4D H15 H15 H 0 1 N N N N N N 8.864  27.692 26.958 -5.008 1.422  0.852  H15 Y4D 47 
Y4D H16 H16 H 0 1 N N N N N N 7.719  28.925 28.477 -9.048 2.083  0.631  H16 Y4D 48 
Y4D H17 H17 H 0 1 N N N N N N 6.071  28.469 29.027 -7.702 2.654  -0.382 H17 Y4D 49 
Y4D H18 H18 H 0 1 N N N N N N 7.020  29.470 26.348 -9.199 1.105  -1.624 H18 Y4D 50 
Y4D H19 H19 H 0 1 N N N N N N 5.567  29.918 27.303 -7.558 0.447  -1.474 H19 Y4D 51 
Y4D H20 H20 H 0 1 N N N N N N 6.035  23.785 25.546 6.396  -2.530 -1.232 H20 Y4D 52 
Y4D H21 H21 H 0 1 N N N N N N 4.851  22.683 26.328 6.241  -4.280 -0.898 H21 Y4D 53 
Y4D H22 H22 H 0 1 N N N N N N 6.542  21.484 27.428 6.080  -3.947 1.431  H22 Y4D 54 
Y4D H23 H23 H 0 1 N N N N N N 7.626  22.850 26.999 6.984  -2.445 1.044  H23 Y4D 55 
Y4D H24 H24 H 0 1 N N N N N N 8.695  21.627 25.367 4.447  -2.420 2.196  H24 Y4D 56 
Y4D H25 H25 H 0 1 N N N N N N 7.094  19.436 26.839 5.941  -0.433 1.788  H25 Y4D 57 
Y4D H26 H26 H 0 1 N N N N N N 8.356  19.059 25.618 5.435  -0.440 0.082  H26 Y4D 58 
Y4D H27 H27 H 0 1 N N N N N N 8.720  20.481 28.290 3.531  -0.177 2.451  H27 Y4D 59 
Y4D S1  S1  S 0 1 N Y N N N N 9.774  17.808 27.306 4.682  2.159  -0.184 S1  Y4D 60 
Y4D H29 H29 H 0 1 N N N N N N 8.333  18.095 28.373 5.073  1.786  2.162  H29 Y4D 61 
Y4D H30 H30 H 0 1 N N N N N N 12.449 21.617 25.814 0.518  -1.234 -0.557 H30 Y4D 62 
Y4D H31 H31 H 0 1 N N N N N N 15.397 22.784 29.405 0.929  -1.034 -3.458 H31 Y4D 63 
Y4D H32 H32 H 0 1 N N N N N N 15.907 21.230 28.660 -0.159 -1.725 -2.230 H32 Y4D 64 
Y4D H33 H33 H 0 1 N N N N N N 16.705 22.764 28.174 -0.803 -1.240 -3.817 H33 Y4D 65 
Y4D H34 H34 H 0 1 N N N N N N 9.724  27.044 24.673 -4.385 -0.733 -1.186 H34 Y4D 66 
Y4D H35 H35 H 0 1 N N N N N N 9.371  25.397 24.049 -4.130 -2.101 -0.076 H35 Y4D 67 
Y4D H36 H36 H 0 1 N N N N N N 8.034  24.881 26.087 -5.420 -0.860 1.679  H36 Y4D 68 
Y4D H37 H37 H 0 1 N N N N N N 5.350  28.604 25.011 -9.233 -1.296 -0.980 H37 Y4D 69 
Y4D H38 H38 H 0 1 N N N N N N 4.271  28.234 26.398 -9.958 -0.266 0.275  H38 Y4D 70 
Y4D H39 H39 H 0 1 N N N N N N 4.998  22.027 23.856 3.977  -3.549 -1.655 H39 Y4D 71 
Y4D H40 H40 H 0 1 N N N N N N 12.855 24.247 26.579 -0.928 0.647  1.146  H40 Y4D 72 
Y4D H41 H41 H 0 1 N N N N N N 10.286 17.674 29.544 2.316  2.262  1.389  H41 Y4D 73 
Y4D O2  O6  O 0 1 N Y N N N N ?      ?      ?      5.914  1.573  -0.583 O2  Y4D 74 
Y4D O1  O7  O 0 1 N Y N N N N ?      ?      ?      3.547  2.131  -1.039 O1  Y4D 75 
Y4D O3  O8  O 0 1 N Y N N N N ?      ?      ?      5.002  3.639  -0.032 O3  Y4D 76 
Y4D H45 H45 H 0 1 N Y N N N N ?      ?      ?      5.262  4.072  -0.856 H45 Y4D 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 
Y4D O01 C02 DOUB N N 1  
Y4D C02 N03 SING N N 2  
Y4D C02 C06 SING N N 3  
Y4D N03 C04 SING N N 4  
Y4D C21 O20 SING N N 5  
Y4D C21 C22 SING N N 6  
Y4D O31 C19 DOUB N N 7  
Y4D C23 C22 SING N N 8  
Y4D C23 C24 SING N N 9  
Y4D O20 C19 SING N N 10 
Y4D C19 N18 SING N N 11 
Y4D C06 C07 SING N N 12 
Y4D C06 C05 SING N N 13 
Y4D C04 C05 SING N N 14 
Y4D C22 C27 SING N N 15 
Y4D C24 C30 SING N N 16 
Y4D C24 C25 SING N N 17 
Y4D C30 C29 SING N N 18 
Y4D C16 C15 SING N N 19 
Y4D N18 C13 SING N N 20 
Y4D C07 C08 SING N N 21 
Y4D C13 C12 SING N N 22 
Y4D C13 C14 SING N N 23 
Y4D C29 C28 SING N N 24 
Y4D N11 C12 SING N N 25 
Y4D N11 C08 SING N N 26 
Y4D C27 C26 SING N N 27 
Y4D C12 O32 DOUB N N 28 
Y4D C15 C14 SING N N 29 
Y4D C15 C17 SING N N 30 
Y4D C25 C26 SING N N 31 
Y4D C08 C09 SING N N 32 
Y4D C26 C28 SING N N 33 
Y4D C09 O10 SING N N 34 
Y4D N11 H1  SING N N 35 
Y4D C14 H2  SING N N 36 
Y4D C14 H3  SING N N 37 
Y4D C15 H4  SING N N 38 
Y4D C16 H5  SING N N 39 
Y4D C16 H6  SING N N 40 
Y4D C16 H7  SING N N 41 
Y4D C23 H8  SING N N 42 
Y4D C23 H9  SING N N 43 
Y4D C24 H10 SING N N 44 
Y4D C25 H11 SING N N 45 
Y4D C25 H12 SING N N 46 
Y4D C26 H13 SING N N 47 
Y4D C27 H14 SING N N 48 
Y4D C27 H15 SING N N 49 
Y4D C28 H16 SING N N 50 
Y4D C28 H17 SING N N 51 
Y4D C29 H18 SING N N 52 
Y4D C29 H19 SING N N 53 
Y4D C04 H20 SING N N 54 
Y4D C04 H21 SING N N 55 
Y4D C05 H22 SING N N 56 
Y4D C05 H23 SING N N 57 
Y4D C06 H24 SING N N 58 
Y4D C07 H25 SING N N 59 
Y4D C07 H26 SING N N 60 
Y4D C08 H27 SING N N 61 
Y4D C09 S1  SING N N 62 
Y4D C09 H29 SING N N 63 
Y4D C13 H30 SING N N 64 
Y4D C17 H31 SING N N 65 
Y4D C17 H32 SING N N 66 
Y4D C17 H33 SING N N 67 
Y4D C21 H34 SING N N 68 
Y4D C21 H35 SING N N 69 
Y4D C22 H36 SING N N 70 
Y4D C30 H37 SING N N 71 
Y4D C30 H38 SING N N 72 
Y4D N03 H39 SING N N 73 
Y4D N18 H40 SING N N 74 
Y4D O10 H41 SING N N 75 
Y4D S1  O2  DOUB N N 76 
Y4D S1  O1  DOUB N N 77 
Y4D S1  O3  SING N N 78 
Y4D O3  H45 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 
Y4D 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" 
Y4D InChIKey         InChI                1.03  PGYROSRJIVXTOE-ZDCSSWJMSA-N                                                                                                                                                                                                               
Y4D 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"                                                                                                                                       
Y4D 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"                                                                                                                                                
Y4D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC2C[C@@H]3CCC[C@@H](C3)C2"                                                                                                                                          
Y4D 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           Y4D 
_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        "(1~{R},2~{S})-2-[[(2~{S})-2-[[(1~{S},5~{R})-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 
Y4D "Create component"   2021-02-03 RCSB 
Y4D "Other modification" 2021-02-04 RCSB 
Y4D "Other modification" 2021-02-08 RCSB 
Y4D "Modify name"        2021-02-09 RCSB 
Y4D "Initial release"    2021-02-17 RCSB 
Y4D "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y4D 
_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      ? 
# 
