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                   2021-02-12
_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
#   #
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.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  10.370  20.433  27.010   2.837  -0.115   0.473  N11  Y4D   1  
Y4D  C12  C1   C  0  1  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  13.305  21.998  27.787   0.661   0.741  -1.406  C14  Y4D   3  
Y4D  C15  C3   C  0  1  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  15.159  21.841  26.041  -0.242   1.421  -3.634  C16  Y4D   5  
Y4D  O20  O1   O  0  1  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   7.005  26.505  25.087  -6.732  -1.465   0.079  C23  Y4D   7  
Y4D  C24  C6   C  0  1  N  N  R   5.735  26.705  25.966  -8.025  -1.066   0.788  C24  Y4D   8  
Y4D  C25  C7   C  0  1  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   7.152  26.893  28.027  -7.133   1.237   1.136  C26  Y4D  10  
Y4D  C27  C9   C  0  1  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   6.798  28.388  28.206  -8.133   1.785   0.117  C28  Y4D  12  
Y4D  C29  C11  C  0  1  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   6.802  21.066  24.469   3.810  -2.575   0.146  C02  Y4D  14  
Y4D  C04  C13  C  0  1  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   6.962  22.071  26.598   6.072  -3.015   0.865  C05  Y4D  16  
Y4D  C06  C15  C  0  1  N  N  S   7.746  21.155  25.661   4.818  -2.175   1.201  C06  Y4D  17  
Y4D  C07  C16  C  0  1  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   9.114  19.853  27.477   3.886   0.128   1.467  C08  Y4D  19  
Y4D  C09  C18  C  0  1  N  N  R   9.323  18.442  28.041   4.233   1.618   1.488  C09  Y4D  20  
Y4D  C13  C19  C  0  1  N  N  S  12.192  22.226  26.693   0.463  -0.200  -0.216  C13  Y4D  21  
Y4D  C17  C20  C  0  1  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  11.041  24.135  25.579  -1.944  -0.562  -0.109  C19  Y4D  23  
Y4D  C21  C22  C  0  1  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   8.233  25.937  25.852  -5.561  -0.645   0.619  C22  Y4D  25  
Y4D  C30  C24  C  0  1  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   5.720  21.947  24.543   4.429  -3.200  -0.871  N03  Y4D  27  
Y4D  N18  N3   N  0  1  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   6.942  20.303  23.517   2.617  -2.368   0.212  O01  Y4D  29  
Y4D  O10  O3   O  0  1  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  10.291  23.378  24.975  -1.844  -1.314  -1.058  O31  Y4D  31  
Y4D  O32  O5   O  0  1  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  10.957  19.844  26.455   3.075  -0.398  -0.424  H1   Y4D  33  
Y4D  H2   H2   H  0  1  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  13.370  20.920  27.998   0.518   1.772  -1.083  H3   Y4D  35  
Y4D  H4   H4   H  0  1  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  16.155  22.219  25.769   0.763   1.387  -4.053  H5   Y4D  37  
Y4D  H6   H6   H  0  1  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  14.443  22.086  25.243  -0.442   2.421  -3.248  H7   Y4D  39  
Y4D  H8   H8   H  0  1  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   6.754  25.808  24.274  -6.832  -1.297  -0.993  H9   Y4D  41  
Y4D  H10  H10  H  0  1  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   5.051  26.391  27.992  -8.667   0.301   2.322  H11  Y4D  43  
Y4D  H12  H12  H  0  1  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   7.321  26.459  29.023  -6.921   2.007   1.882  H13  Y4D  45  
Y4D  H14  H14  H  0  1  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   8.864  27.692  26.958  -5.008   1.422   0.852  H15  Y4D  47  
Y4D  H16  H16  H  0  1  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   6.071  28.469  29.027  -7.702   2.654  -0.382  H17  Y4D  49  
Y4D  H18  H18  H  0  1  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   5.567  29.918  27.303  -7.558   0.447  -1.474  H19  Y4D  51  
Y4D  H20  H20  H  0  1  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   4.851  22.683  26.328   6.241  -4.280  -0.898  H21  Y4D  53  
Y4D  H22  H22  H  0  1  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   7.626  22.850  26.999   6.984  -2.445   1.044  H23  Y4D  55  
Y4D  H24  H24  H  0  1  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   7.094  19.436  26.839   5.941  -0.433   1.788  H25  Y4D  57  
Y4D  H26  H26  H  0  1  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   8.720  20.481  28.290   3.531  -0.177   2.451  H27  Y4D  59  
Y4D  S1   S1   S  0  1  N  Y  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   8.333  18.095  28.373   5.073   1.786   2.162  H29  Y4D  61  
Y4D  H30  H30  H  0  1  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  15.397  22.784  29.405   0.929  -1.034  -3.458  H31  Y4D  63  
Y4D  H32  H32  H  0  1  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  16.705  22.764  28.174  -0.803  -1.240  -3.817  H33  Y4D  65  
Y4D  H34  H34  H  0  1  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   9.371  25.397  24.049  -4.130  -2.101  -0.076  H35  Y4D  67  
Y4D  H36  H36  H  0  1  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   5.350  28.604  25.011  -9.233  -1.296  -0.980  H37  Y4D  69  
Y4D  H38  H38  H  0  1  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   4.998  22.027  23.856   3.977  -3.549  -1.655  H39  Y4D  71  
Y4D  H40  H40  H  0  1  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  10.286  17.674  29.544   2.316   2.262   1.389  H41  Y4D  73  
Y4D  O2   O6   O  0  1  N  Y  N       ?       ?       ?   5.914   1.573  -0.583  O2   Y4D  74  
Y4D  O1   O7   O  0  1  N  Y  N       ?       ?       ?   3.547   2.131  -1.039  O1   Y4D  75  
Y4D  O3   O8   O  0  1  N  Y  N       ?       ?       ?   5.002   3.639  -0.032  O3   Y4D  76  
Y4D  H45  H45  H  0  1  N  Y  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  
##
