data_Y8S
# 
_chem_comp.id                                    Y8S 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-(((((1R,3S,5S)-bicyclo[3.3.1]non-6-en-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 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                     2021-02-10 
_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                        529.647 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y8S 
_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        7LKW 
_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 
Y8S N11 N1  N 0 1 N N N N N N 10.291 20.257 27.254 2.540  -0.337 -0.141 N11 Y8S 1  
Y8S C12 C1  C 0 1 N N N N N N 10.777 21.511 27.694 1.269  0.105  -0.057 C12 Y8S 2  
Y8S C14 C2  C 0 1 N N N N N N 13.258 21.789 28.161 0.341  -1.010 -2.068 C14 Y8S 3  
Y8S N18 N2  N 0 1 N N N N N N 12.070 23.456 26.814 -1.132 -0.050 -0.368 N18 Y8S 4  
Y8S C19 C3  C 0 1 N N N N N N 11.158 23.912 25.950 -2.278 -0.753 -0.267 C19 Y8S 5  
Y8S C21 C4  C 0 1 N N N N N N 9.965  25.795 25.020 -4.640 -0.933 0.021  C21 Y8S 6  
Y8S C22 C5  C 0 1 N N S N N N 10.402 27.027 24.204 -5.861 -0.035 0.234  C22 Y8S 7  
Y8S C23 C6  C 0 1 N N N N N N 9.300  27.631 23.300 -7.129 -0.886 0.214  C23 Y8S 8  
Y8S C24 C7  C 0 1 N N R N N N 8.429  28.704 23.963 -8.360 -0.039 0.498  C24 Y8S 9  
Y8S C25 C8  C 0 1 N N N N N N 8.385  28.524 25.479 -8.216 0.711  1.823  C25 Y8S 10 
Y8S C26 C9  C 0 1 N N S N N N 9.787  28.786 25.978 -6.966 1.595  1.746  C26 Y8S 11 
Y8S C27 C10 C 0 1 N N N N N N 10.868 28.148 25.104 -5.743 0.676  1.586  C27 Y8S 12 
Y8S C02 C11 C 0 1 N N N N N N 6.698  20.953 24.720 3.512  -2.155 1.599  C02 Y8S 13 
Y8S C04 C12 C 0 1 N N N N N N 5.665  22.580 26.161 5.517  -3.327 1.541  C04 Y8S 14 
Y8S C05 C13 C 0 1 N N N N N N 6.846  21.955 26.929 5.835  -1.982 2.231  C05 Y8S 15 
Y8S C06 C14 C 0 1 N N S N N N 7.608  21.037 25.948 4.598  -1.134 1.855  C06 Y8S 16 
Y8S C07 C15 C 0 1 N N N N N N 7.928  19.665 26.560 4.873  -0.316 0.591  C07 Y8S 17 
Y8S C08 C16 C 0 1 N N S N N N 8.990  19.720 27.723 3.647  0.536  0.258  C08 Y8S 18 
Y8S C09 C17 C 0 1 N N R N N N 9.172  18.286 28.233 3.985  1.489  -0.890 C09 Y8S 19 
Y8S C13 C18 C 0 1 N N S N N N 12.149 22.026 27.148 0.139  -0.748 -0.574 C13 Y8S 20 
Y8S C15 C19 C 0 1 N N N N N N 14.602 22.318 27.709 -0.736 -1.976 -2.566 C15 Y8S 21 
Y8S C16 C20 C 0 1 N N N N N N 15.677 22.137 28.801 -0.611 -2.142 -4.082 C16 Y8S 22 
Y8S C17 C21 C 0 1 N N N N N N 15.066 21.641 26.425 -0.554 -3.336 -1.887 C17 Y8S 23 
Y8S C28 C22 C 0 1 N N N N N N 9.898  30.250 25.893 -7.056 2.472  0.525  C28 Y8S 24 
Y8S C29 C23 C 0 1 N N N N N N 9.569  30.847 24.756 -7.785 2.184  -0.504 C29 Y8S 25 
Y8S C30 C24 C 0 1 N N N N N N 8.929  30.130 23.597 -8.639 0.949  -0.626 C30 Y8S 26 
Y8S N03 N3  N 0 1 N N N N N N 5.631  21.840 24.909 4.054  -3.374 1.433  N03 Y8S 27 
Y8S O01 O1  O 0 1 N N N N N N 6.839  20.268 23.749 2.325  -1.911 1.556  O01 Y8S 28 
Y8S O10 O2  O 0 1 N N N N N N 9.914  18.412 29.397 4.506  0.743  -1.991 O10 Y8S 29 
Y8S O20 O3  O 0 1 N N N N N N 10.941 25.264 25.919 -3.447 -0.112 -0.078 O20 Y8S 30 
Y8S O31 O4  O 0 1 N N N N N N 10.541 23.174 25.221 -2.256 -1.965 -0.347 O31 Y8S 31 
Y8S O32 O5  O 0 1 N N N N N N 10.139 22.202 28.447 1.035  1.188  0.435  O32 Y8S 32 
Y8S H1  H1  H 0 1 N N N N N N 10.838 19.720 26.612 2.721  -1.234 -0.463 H1  Y8S 33 
Y8S H2  H2  H 0 1 N N N N N N 12.984 22.288 29.102 0.267  -0.071 -2.615 H2  Y8S 34 
Y8S H3  H3  H 0 1 N N N N N N 13.348 20.706 28.333 1.326  -1.449 -2.230 H3  Y8S 35 
Y8S H4  H4  H 0 1 N N N N N N 12.708 24.097 27.240 -1.150 0.918  -0.304 H4  Y8S 36 
Y8S H5  H5  H 0 1 N N N N N N 9.081  26.078 25.611 -4.542 -1.617 0.864  H5  Y8S 37 
Y8S H6  H6  H 0 1 N N N N N N 9.692  25.000 24.310 -4.765 -1.505 -0.898 H6  Y8S 38 
Y8S H7  H7  H 0 1 N N N N N N 11.242 26.728 23.560 -5.909 0.707  -0.563 H7  Y8S 39 
Y8S H8  H8  H 0 1 N N N N N N 8.642  26.813 22.972 -7.233 -1.350 -0.767 H8  Y8S 40 
Y8S H9  H9  H 0 1 N N N N N N 9.788  28.082 22.424 -7.049 -1.666 0.971  H9  Y8S 41 
Y8S H10 H10 H 0 1 N N N N N N 7.405  28.598 23.576 -9.220 -0.704 0.575  H10 Y8S 42 
Y8S H11 H11 H 0 1 N N N N N N 7.681  29.241 25.927 -9.096 1.332  1.990  H11 Y8S 43 
Y8S H12 H12 H 0 1 N N N N N N 8.076  27.499 25.732 -8.110 -0.004 2.639  H12 Y8S 44 
Y8S H13 H13 H 0 1 N N N N N N 9.892  28.444 27.018 -6.872 2.203  2.646  H13 Y8S 45 
Y8S H14 H14 H 0 1 N N N N N N 11.647 27.747 25.768 -5.729 -0.061 2.389  H14 Y8S 46 
Y8S H15 H15 H 0 1 N N N N N N 11.298 28.936 24.468 -4.829 1.269  1.613  H15 Y8S 47 
Y8S H16 H16 H 0 1 N N N N N N 5.840  23.651 25.978 5.970  -3.359 0.550  H16 Y8S 48 
Y8S H17 H17 H 0 1 N N N N N N 6.471  21.366 27.779 5.910  -2.105 3.312  H17 Y8S 49 
Y8S H18 H18 H 0 1 N N N N N N 7.515  22.747 27.298 6.747  -1.543 1.827  H18 Y8S 50 
Y8S H19 H19 H 0 1 N N N N N N 8.550  21.528 25.662 4.318  -0.478 2.679  H19 Y8S 51 
Y8S H20 H20 H 0 1 N N N N N N 6.997  19.238 26.961 5.732  0.333  0.759  H20 Y8S 52 
Y8S H21 H21 H 0 1 N N N N N N 8.318  19.013 25.765 5.083  -0.991 -0.239 H21 Y8S 53 
Y8S H22 H22 H 0 1 N N N N N N 8.594  20.348 28.535 3.356  1.113  1.136  H22 Y8S 54 
Y8S S1  S1  S 0 1 N Y N N N N 9.685  17.684 27.513 5.224  2.691  -0.332 S1  Y8S 55 
Y8S H24 H24 H 0 1 N N N N N N 8.170  17.917 28.497 3.083  2.016  -1.202 H24 Y8S 56 
Y8S H25 H25 H 0 1 N N N N N N 12.384 21.457 26.236 0.124  -1.696 -0.037 H25 Y8S 57 
Y8S H26 H26 H 0 1 N N N N N N 14.500 23.395 27.510 -1.721 -1.578 -2.323 H26 Y8S 58 
Y8S H27 H27 H 0 1 N N N N N N 15.344 22.625 29.729 0.374  -2.540 -4.324 H27 Y8S 59 
Y8S H28 H28 H 0 1 N N N N N N 15.833 21.064 28.987 -1.378 -2.830 -4.436 H28 Y8S 60 
Y8S H29 H29 H 0 1 N N N N N N 16.620 22.592 28.466 -0.741 -1.173 -4.565 H29 Y8S 61 
Y8S H30 H30 H 0 1 N N N N N N 16.043 22.049 26.127 -0.643 -3.218 -0.808 H30 Y8S 62 
Y8S H31 H31 H 0 1 N N N N N N 15.157 20.558 26.594 -1.321 -4.024 -2.242 H31 Y8S 63 
Y8S H32 H32 H 0 1 N N N N N N 14.332 21.827 25.627 0.431  -3.734 -2.130 H32 Y8S 64 
Y8S H33 H33 H 0 1 N N N N N N 10.240 30.827 26.739 -6.483 3.388  0.507  H33 Y8S 65 
Y8S H34 H34 H 0 1 N N N N N N 9.771  31.903 24.656 -7.766 2.869  -1.339 H34 Y8S 66 
Y8S H35 H35 H 0 1 N N N N N N 9.668  30.045 22.787 -8.450 0.464  -1.583 H35 Y8S 67 
Y8S H36 H36 H 0 1 N N N N N N 8.071  30.723 23.249 -9.686 1.252  -0.582 H36 Y8S 68 
Y8S H37 H37 H 0 1 N N N N N N 10.066 17.552 29.771 3.895  0.080  -2.341 H37 Y8S 69 
Y8S O1  O6  O 0 1 N Y N N N N ?      ?      ?      6.394  2.025  0.124  O1  Y8S 70 
Y8S O2  O7  O 0 1 N Y N N N N ?      ?      ?      5.308  3.779  -1.243 O2  Y8S 71 
Y8S O3  O8  O 0 1 N Y N N N N ?      ?      ?      4.624  3.300  0.926  O3  Y8S 72 
Y8S H23 H23 H 0 1 N N N N N N 4.725  22.452 26.717 5.878  -4.157 2.148  H23 Y8S 73 
Y8S H38 H38 H 0 1 N N N N N N 4.901  21.956 24.235 3.544  -4.181 1.263  H38 Y8S 74 
Y8S H39 H39 H 0 1 N Y N N N N ?      ?      ?      5.182  3.971  1.343  H39 Y8S 75 
# 
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 
Y8S C23 C24 SING N N 1  
Y8S C23 C22 SING N N 2  
Y8S C30 C24 SING N N 3  
Y8S C30 C29 SING N N 4  
Y8S O01 C02 DOUB N N 5  
Y8S C24 C25 SING N N 6  
Y8S C22 C21 SING N N 7  
Y8S C22 C27 SING N N 8  
Y8S C02 N03 SING N N 9  
Y8S C02 C06 SING N N 10 
Y8S C29 C28 DOUB N N 11 
Y8S N03 C04 SING N N 12 
Y8S C21 O20 SING N N 13 
Y8S C27 C26 SING N N 14 
Y8S O31 C19 DOUB N N 15 
Y8S C25 C26 SING N N 16 
Y8S C28 C26 SING N N 17 
Y8S O20 C19 SING N N 18 
Y8S C06 C07 SING N N 19 
Y8S C06 C05 SING N N 20 
Y8S C19 N18 SING N N 21 
Y8S C04 C05 SING N N 22 
Y8S C17 C15 SING N N 23 
Y8S C07 C08 SING N N 24 
Y8S N18 C13 SING N N 25 
Y8S C13 C12 SING N N 26 
Y8S C13 C14 SING N N 27 
Y8S N11 C12 SING N N 28 
Y8S N11 C08 SING N N 29 
Y8S C12 O32 DOUB N N 30 
Y8S C15 C14 SING N N 31 
Y8S C15 C16 SING N N 32 
Y8S C08 C09 SING N N 33 
Y8S C09 O10 SING N N 34 
Y8S N11 H1  SING N N 35 
Y8S C14 H2  SING N N 36 
Y8S C14 H3  SING N N 37 
Y8S N18 H4  SING N N 38 
Y8S C21 H5  SING N N 39 
Y8S C21 H6  SING N N 40 
Y8S C22 H7  SING N N 41 
Y8S C23 H8  SING N N 42 
Y8S C23 H9  SING N N 43 
Y8S C24 H10 SING N N 44 
Y8S C25 H11 SING N N 45 
Y8S C25 H12 SING N N 46 
Y8S C26 H13 SING N N 47 
Y8S C27 H14 SING N N 48 
Y8S C27 H15 SING N N 49 
Y8S C04 H16 SING N N 50 
Y8S C05 H17 SING N N 51 
Y8S C05 H18 SING N N 52 
Y8S C06 H19 SING N N 53 
Y8S C07 H20 SING N N 54 
Y8S C07 H21 SING N N 55 
Y8S C08 H22 SING N N 56 
Y8S C09 S1  SING N N 57 
Y8S C09 H24 SING N N 58 
Y8S C13 H25 SING N N 59 
Y8S C15 H26 SING N N 60 
Y8S C16 H27 SING N N 61 
Y8S C16 H28 SING N N 62 
Y8S C16 H29 SING N N 63 
Y8S C17 H30 SING N N 64 
Y8S C17 H31 SING N N 65 
Y8S C17 H32 SING N N 66 
Y8S C28 H33 SING N N 67 
Y8S C29 H34 SING N N 68 
Y8S C30 H35 SING N N 69 
Y8S C30 H36 SING N N 70 
Y8S O10 H37 SING N N 71 
Y8S S1  O1  DOUB N N 72 
Y8S S1  O2  DOUB N N 73 
Y8S S1  O3  SING N N 74 
Y8S C04 H23 SING N N 75 
Y8S N03 H38 SING N N 76 
Y8S O3  H39 SING N N 77 
# 
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 
Y8S InChI            InChI                1.03  "InChI=1S/C24H39N3O8S/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/h3-4,14-20,23,30H,5-13H2,1-2H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t15-,16+,17+,18-,19-,20-,23+/m0/s1" 
Y8S InChIKey         InChI                1.03  ZIWRGXZFSGDQST-REFFYEJJSA-N                                                                                                                                                                                                                   
Y8S SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OC[C@H]1C[C@@H]2CC=C[C@H](C1)C2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                         
Y8S SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OC[CH]1C[CH]2CC=C[CH](C1)C2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O"                                                                                                                                                   
Y8S 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)OC[C@H]2C[C@@H]3CC=C[C@@H](C3)C2"                                                                                                                                             
Y8S SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CC3CC=CC(C3)C2"                                                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           Y8S 
_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},3~{S},5~{S})-3-bicyclo[3.3.1]non-6-enyl]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 
Y8S "Create component" 2021-02-10 RCSB 
Y8S "Initial release"  2021-02-17 RCSB 
Y8S "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y8S 
_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      ? 
# 
