data_Y5S
# 
_chem_comp.id                                    Y5S 
_chem_comp.name                                  "(1S,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                     2021-02-04 
_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                     Y5S 
_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 
Y5S C17 C1  C 0 1 N N N N N N 15.997 22.218 28.334 -1.165 3.482  3.367  C17 Y5S 1  
Y5S C13 C2  C 0 1 N N S N N N 12.272 22.250 26.895 0.079  0.714  1.003  C13 Y5S 2  
Y5S C14 C3  C 0 1 N N N N N N 13.459 22.068 27.907 0.092  2.046  1.755  C14 Y5S 3  
Y5S C15 C4  C 0 1 N N N N N N 14.840 22.510 27.344 -1.089 2.095  2.726  C15 Y5S 4  
Y5S C21 C5  C 0 1 N N N N N N 9.568  25.928 24.959 4.661  -0.734 0.636  C21 Y5S 5  
Y5S C23 C6  C 0 1 N N N N N N 7.017  26.495 25.084 6.964  -1.617 0.279  C23 Y5S 6  
Y5S C24 C7  C 0 1 N N R N N N 5.741  26.697 25.955 8.234  -1.494 -0.557 C24 Y5S 7  
Y5S C26 C8  C 0 1 N N S N N N 7.153  26.881 28.020 7.353  0.394  -1.897 C26 Y5S 8  
Y5S C12 C9  C 0 1 N N N N N N 10.983 21.588 27.469 -1.122 0.661  0.095  C12 Y5S 9  
Y5S C16 C10 C 0 1 N N N N N N 15.133 21.885 25.962 -0.898 1.039  3.816  C16 Y5S 10 
Y5S C09 C11 C 0 1 N N S N N N 9.407  18.563 28.000 -4.169 1.546  -0.498 C09 Y5S 11 
Y5S C08 C12 C 0 1 N N S N N N 9.141  19.921 27.346 -3.481 0.194  -0.299 C08 Y5S 12 
Y5S C06 C13 C 0 1 N N S N N N 7.702  21.114 25.557 -3.794 -2.158 0.483  C06 Y5S 13 
Y5S C02 C14 C 0 1 N N N N N N 6.708  20.991 24.416 -4.758 -3.160 1.080  C02 Y5S 14 
Y5S C04 C15 C 0 1 N N N N N N 5.792  22.712 25.710 -3.693 -4.261 -0.666 C04 Y5S 15 
Y5S C07 C16 C 0 1 N N N N N N 8.082  19.761 26.244 -4.472 -0.797 0.315  C07 Y5S 16 
Y5S C05 C17 C 0 1 N N N N N N 6.909  21.980 26.535 -3.432 -2.756 -0.897 C05 Y5S 17 
Y5S C19 C18 C 0 1 N N N N N N 11.085 24.129 25.698 2.411  0.054  0.746  C19 Y5S 18 
Y5S C22 C19 C 0 1 N N S N N N 8.234  25.909 25.853 5.797  -0.891 -0.385 C22 Y5S 19 
Y5S C25 C20 C 0 1 N N N N N N 5.949  26.183 27.383 7.873  -1.044 -1.972 C25 Y5S 20 
Y5S C27 C21 C 0 1 N N N N N N 8.452  26.678 27.185 6.182  0.480  -0.921 C27 Y5S 21 
Y5S C28 C22 C 0 1 N N N N N N 6.806  28.378 28.196 8.485  1.295  -1.387 C28 Y5S 22 
Y5S C29 C23 C 0 1 N N N N N N 6.197  29.072 26.943 8.837  0.887  0.044  C29 Y5S 23 
Y5S C30 C24 C 0 1 N N N N N N 5.315  28.184 26.017 9.259  -0.578 0.088  C30 Y5S 24 
Y5S N03 N1  N 0 1 N N N N N N 5.637  21.885 24.511 -4.684 -4.325 0.415  N03 Y5S 25 
Y5S N11 N2  N 0 1 N N N N N N 10.350 20.542 26.849 -2.335 0.357  0.599  N11 Y5S 26 
Y5S N18 N3  N 0 1 N N N N N N 12.052 23.677 26.604 1.301  0.593  0.203  N18 Y5S 27 
Y5S O01 O1  O 0 1 N N N N N N 6.799  20.191 23.489 -5.490 -2.942 2.022  O01 Y5S 28 
Y5S O10 O2  O 0 1 N N N N N N 8.187  18.025 28.468 -3.214 2.504  -0.958 O10 Y5S 29 
Y5S O20 O3  O 0 1 N N N N N N 10.803 25.492 25.588 3.502  -0.151 -0.016 O20 Y5S 30 
Y5S O31 O4  O 0 1 N N N N N N 10.463 23.334 25.004 2.427  -0.245 1.924  O31 Y5S 31 
Y5S O32 O5  O 0 1 N N N N N N 10.496 22.052 28.512 -0.998 0.892  -1.089 O32 Y5S 32 
Y5S H1  H1  H 0 1 N N N N N N 15.768 22.671 29.310 -1.301 4.235  2.590  H1  Y5S 33 
Y5S H2  H2  H 0 1 N N N N N N 16.112 21.131 28.453 -2.007 3.517  4.059  H2  Y5S 34 
Y5S H3  H3  H 0 1 N N N N N N 16.932 22.645 27.942 -0.241 3.683  3.909  H3  Y5S 35 
Y5S H4  H4  H 0 1 N N N N N N 12.538 21.728 25.964 0.031  -0.107 1.718  H4  Y5S 36 
Y5S H5  H5  H 0 1 N N N N N N 13.244 22.666 28.805 1.024  2.140  2.312  H5  Y5S 37 
Y5S H6  H6  H 0 1 N N N N N N 13.521 21.004 28.181 0.011  2.867  1.042  H6  Y5S 38 
Y5S H7  H7  H 0 1 N N N N N N 14.799 23.601 27.206 -2.013 1.895  2.184  H7  Y5S 39 
Y5S H8  H8  H 0 1 N N N N N N 9.720  26.962 24.616 4.398  -1.711 1.039  H8  Y5S 40 
Y5S H9  H9  H 0 1 N N N N N N 9.392  25.276 24.091 4.988  -0.082 1.446  H9  Y5S 41 
Y5S H10 H10 H 0 1 N N N N N N 7.309  27.472 24.671 6.710  -2.674 0.399  H10 Y5S 42 
Y5S H11 H11 H 0 1 N N N N N N 6.767  25.809 24.262 7.139  -1.189 1.270  H11 Y5S 43 
Y5S H12 H12 H 0 1 N N N N N N 4.921  26.124 25.497 8.680  -2.503 -0.635 H12 Y5S 44 
Y5S H13 H13 H 0 1 N N N N N N 7.318  26.447 29.017 7.041  0.725  -2.884 H13 Y5S 45 
Y5S H14 H14 H 0 1 N N N N N N 16.117 22.225 25.606 -0.007 1.275  4.398  H14 Y5S 46 
Y5S H15 H15 H 0 1 N N N N N N 15.134 20.788 26.048 -1.769 1.031  4.471  H15 Y5S 47 
Y5S H16 H16 H 0 1 N N N N N N 14.357 22.196 25.247 -0.781 0.058  3.355  H16 Y5S 48 
Y5S H17 H17 H 0 1 N N N N N N 10.051 18.754 28.871 -4.593 1.882  0.449  H17 Y5S 49 
Y5S S1  S1  S 0 1 N Y N N N N 9.834  17.899 27.278 -5.494 1.375  -1.726 S1  Y5S 50 
Y5S H19 H19 H 0 1 N N N N N N 8.710  20.575 28.118 -3.138 -0.184 -1.261 H19 Y5S 51 
Y5S H20 H20 H 0 1 N N N N N N 8.611  21.638 25.226 -2.903 -2.066 1.104  H20 Y5S 52 
Y5S H21 H21 H 0 1 N N N N N N 6.108  23.732 25.444 -4.093 -4.718 -1.571 H21 Y5S 53 
Y5S H22 H22 H 0 1 N N N N N N 4.851  22.756 26.279 -2.773 -4.762 -0.365 H22 Y5S 54 
Y5S H23 H23 H 0 1 N N N N N N 7.175  19.328 26.691 -4.797 -0.430 1.289  H23 Y5S 55 
Y5S H24 H24 H 0 1 N N N N N N 8.475  19.077 25.477 -5.336 -0.900 -0.341 H24 Y5S 56 
Y5S H25 H25 H 0 1 N N N N N N 6.451  21.349 27.311 -4.085 -2.362 -1.676 H25 Y5S 57 
Y5S H26 H26 H 0 1 N N N N N N 7.573  22.719 27.008 -2.385 -2.574 -1.138 H26 Y5S 58 
Y5S H27 H27 H 0 1 N N N N N N 8.013  24.859 26.096 5.424  -1.507 -1.213 H27 Y5S 59 
Y5S H28 H28 H 0 1 N N N N N N 5.049  26.392 27.980 8.760  -1.077 -2.603 H28 Y5S 60 
Y5S H29 H29 H 0 1 N N N N N N 6.128  25.098 27.357 7.104  -1.693 -2.385 H29 Y5S 61 
Y5S H30 H30 H 0 1 N N N N N N 9.171  26.113 27.796 6.429  1.150  -0.098 H30 Y5S 62 
Y5S H31 H31 H 0 1 N N N N N N 8.869  27.668 26.948 5.320  0.909  -1.450 H31 Y5S 63 
Y5S H32 H32 H 0 1 N N N N N N 7.730  28.912 28.465 9.358  1.176  -2.027 H32 Y5S 64 
Y5S H33 H33 H 0 1 N N N N N N 6.080  28.464 29.018 8.156  2.332  -1.403 H33 Y5S 65 
Y5S H34 H34 H 0 1 N N N N N N 7.030  29.461 26.339 9.667  1.509  0.394  H34 Y5S 66 
Y5S H35 H35 H 0 1 N N N N N N 5.576  29.909 27.294 7.986  1.049  0.702  H35 Y5S 67 
Y5S H36 H36 H 0 1 N N N N N N 5.362  28.597 24.999 9.408  -0.875 1.132  H36 Y5S 68 
Y5S H37 H37 H 0 1 N N N N N N 4.279  28.229 26.383 10.220 -0.686 -0.430 H37 Y5S 69 
Y5S H38 H38 H 0 1 N N N N N N 4.881  21.950 23.860 -5.218 -5.109 0.623  H38 Y5S 70 
Y5S H39 H39 H 0 1 N N N N N N 10.747 20.187 26.003 -2.448 0.247  1.556  H39 Y5S 71 
Y5S H40 H40 H 0 1 N N N N N N 12.619 24.353 27.075 1.311  0.900  -0.717 H40 Y5S 72 
Y5S H41 H41 H 0 1 N N N N N N 8.348  17.182 28.875 -2.476 2.646  -0.350 H41 Y5S 73 
Y5S O1  O6  O 0 1 N Y N N N N ?      ?      ?      -6.182 2.607  -1.891 O1  Y5S 74 
Y5S O2  O7  O 0 1 N Y N N N N ?      ?      ?      -5.039 0.633  -2.849 O2  Y5S 75 
Y5S O3  O8  O 0 1 N Y N N N N ?      ?      ?      -6.513 0.462  -1.060 O3  Y5S 76 
Y5S H18 H18 H 0 1 N Y N N N N ?      ?      ?      -7.290 0.277  -1.605 H18 Y5S 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 
Y5S O01 C02 DOUB N N 1  
Y5S C02 N03 SING N N 2  
Y5S C02 C06 SING N N 3  
Y5S N03 C04 SING N N 4  
Y5S C21 O20 SING N N 5  
Y5S C21 C22 SING N N 6  
Y5S O31 C19 DOUB N N 7  
Y5S C23 C22 SING N N 8  
Y5S C23 C24 SING N N 9  
Y5S C06 C07 SING N N 10 
Y5S C06 C05 SING N N 11 
Y5S O20 C19 SING N N 12 
Y5S C19 N18 SING N N 13 
Y5S C04 C05 SING N N 14 
Y5S C22 C27 SING N N 15 
Y5S C24 C30 SING N N 16 
Y5S C24 C25 SING N N 17 
Y5S C16 C15 SING N N 18 
Y5S C30 C29 SING N N 19 
Y5S C07 C08 SING N N 20 
Y5S N18 C13 SING N N 21 
Y5S N11 C08 SING N N 22 
Y5S N11 C12 SING N N 23 
Y5S C13 C12 SING N N 24 
Y5S C13 C14 SING N N 25 
Y5S C29 C28 SING N N 26 
Y5S C27 C26 SING N N 27 
Y5S C15 C14 SING N N 28 
Y5S C15 C17 SING N N 29 
Y5S C08 C09 SING N N 30 
Y5S C25 C26 SING N N 31 
Y5S C12 O32 DOUB N N 32 
Y5S C09 O10 SING N N 33 
Y5S C26 C28 SING N N 34 
Y5S C17 H1  SING N N 35 
Y5S C17 H2  SING N N 36 
Y5S C17 H3  SING N N 37 
Y5S C13 H4  SING N N 38 
Y5S C14 H5  SING N N 39 
Y5S C14 H6  SING N N 40 
Y5S C15 H7  SING N N 41 
Y5S C21 H8  SING N N 42 
Y5S C21 H9  SING N N 43 
Y5S C23 H10 SING N N 44 
Y5S C23 H11 SING N N 45 
Y5S C24 H12 SING N N 46 
Y5S C26 H13 SING N N 47 
Y5S C16 H14 SING N N 48 
Y5S C16 H15 SING N N 49 
Y5S C16 H16 SING N N 50 
Y5S C09 H17 SING N N 51 
Y5S C09 S1  SING N N 52 
Y5S C08 H19 SING N N 53 
Y5S C06 H20 SING N N 54 
Y5S C04 H21 SING N N 55 
Y5S C04 H22 SING N N 56 
Y5S C07 H23 SING N N 57 
Y5S C07 H24 SING N N 58 
Y5S C05 H25 SING N N 59 
Y5S C05 H26 SING N N 60 
Y5S C22 H27 SING N N 61 
Y5S C25 H28 SING N N 62 
Y5S C25 H29 SING N N 63 
Y5S C27 H30 SING N N 64 
Y5S C27 H31 SING N N 65 
Y5S C28 H32 SING N N 66 
Y5S C28 H33 SING N N 67 
Y5S C29 H34 SING N N 68 
Y5S C29 H35 SING N N 69 
Y5S C30 H36 SING N N 70 
Y5S C30 H37 SING N N 71 
Y5S N03 H38 SING N N 72 
Y5S N11 H39 SING N N 73 
Y5S N18 H40 SING N N 74 
Y5S O10 H41 SING N N 75 
Y5S S1  O1  DOUB N N 76 
Y5S S1  O2  DOUB N N 77 
Y5S S1  O3  SING N N 78 
Y5S O3  H18 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 
Y5S SMILES           ACDLabs              12.01 "CC(CC(C(=O)NC(C(O)S(=O)(=O)O)CC1CCNC1=O)NC(OCC3CC2CCCC(C2)C3)=O)C"                                                                                                                                                                       
Y5S 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" 
Y5S InChIKey         InChI                1.03  PGYROSRJIVXTOE-LZHMTVEHSA-N                                                                                                                                                                                                               
Y5S 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"                                                                                                                                      
Y5S 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"                                                                                                                                                
Y5S 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"                                                                                                                                         
Y5S 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"                                                                                                                                                                       
# 
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 
Y5S "SYSTEMATIC NAME" ACDLabs              12.01 "(1S,2S)-2-{[N-({[(3-endo)-bicyclo[3.3.1]nonan-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid"                                              
Y5S "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{S},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 
Y5S "Create component"   2021-02-04 RCSB 
Y5S "Other modification" 2021-02-04 RCSB 
Y5S "Modify name"        2021-02-09 RCSB 
Y5S "Initial release"    2021-02-17 RCSB 
Y5S "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y5S 
_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      ? 
# 
