data_ZPA
#

_chem_comp.id                                   ZPA
_chem_comp.name                                 "4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C26 H37 N3 O11 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2
S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-01-31
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       599.650
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ZPA
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       3WQ6
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
ZPA  C13    C13    C  0  1  Y  N  N  -1.323  31.563  18.016    8.994   1.008  -1.413  C13    ZPA   1  
ZPA  C14    C14    C  0  1  Y  N  N  -0.340  30.864  18.711    9.853   0.925  -2.493  C14    ZPA   2  
ZPA  C15    C15    C  0  1  Y  N  N  -0.452  30.675  20.084   10.979   0.126  -2.421  C15    ZPA   3  
ZPA  C16    C16    C  0  1  Y  N  N  -1.554  31.184  20.764   11.245  -0.591  -1.269  C16    ZPA   4  
ZPA  C17    C17    C  0  1  Y  N  N  -2.529  31.890  20.066   10.385  -0.509  -0.189  C17    ZPA   5  
ZPA  C12    C12    C  0  1  Y  N  N  -2.416  32.093  18.692    9.260   0.290  -0.262  C12    ZPA   6  
ZPA  C11    C11    C  0  1  N  N  N  -3.521  32.838  17.920    8.323   0.380   0.915  C11    ZPA   7  
ZPA  N8     N8     N  0  1  N  N  N  -3.435  34.308  17.756    7.294  -0.656   0.800  N8     ZPA   8  
ZPA  C7     C7     C  0  1  N  N  N  -2.603  34.826  16.735    6.133  -0.458   0.163  C7     ZPA   9  
ZPA  O7     O7     O  0  1  N  N  N  -2.205  34.196  15.757    5.798   0.573  -0.381  O7     ZPA  10  
ZPA  C9     C9     C  0  1  N  N  N  -3.322  35.143  18.886    7.439  -1.883   1.318  C9     ZPA  11  
ZPA  O9     O9     O  0  1  N  N  N  -3.426  34.810  20.067    8.410  -2.276   1.928  O9     ZPA  12  
ZPA  C10    C10    C  0  1  N  N  N  -3.022  36.560  18.381    6.200  -2.698   1.021  C10    ZPA  13  
ZPA  C6     C6     C  0  1  N  N  R  -2.350  36.326  17.011    5.305  -1.722   0.230  C6     ZPA  14  
ZPA  S5     S5     S  0  1  N  N  N  -0.556  36.742  17.063    3.749  -1.421   1.112  S5     ZPA  15  
ZPA  C4     C4     C  0  1  N  N  N   0.119  35.290  17.951    2.868  -0.284   0.006  C4     ZPA  16  
ZPA  C3     C3     C  0  1  N  N  N   0.054  35.342  19.489    1.511   0.073   0.617  C3     ZPA  17  
ZPA  C2     C2     C  0  1  N  N  N   0.563  33.995  20.014    0.768   1.032  -0.315  C2     ZPA  18  
ZPA  C1     C1     C  0  1  N  N  N   0.332  33.720  21.508   -0.568   1.383   0.287  C1     ZPA  19  
ZPA  N2     N2     N  0  1  N  N  N  -0.715  34.224  22.123   -0.915   0.882   1.428  N2     ZPA  20  
ZPA  N1     N1     N  0  1  N  N  N   1.197  32.928  22.114   -1.415   2.234  -0.374  N1     ZPA  21  
ZPA  "C1'"  "C1'"  C  0  1  N  N  R   1.150  32.548  23.514   -2.713   2.576   0.212  "C1'"  ZPA  22  
ZPA  "O5'"  "O5'"  O  0  1  N  N  N  -0.216  32.266  23.850   -3.718   1.710  -0.320  "O5'"  ZPA  23  
ZPA  "C2'"  "C2'"  C  0  1  N  N  R   1.907  33.625  24.338   -3.060   4.028  -0.129  "C2'"  ZPA  24  
ZPA  "O2'"  "O2'"  O  0  1  N  N  N   3.292  33.270  24.453   -2.088   4.899   0.451  "O2'"  ZPA  25  
ZPA  "C3'"  "C3'"  C  0  1  N  N  S   1.328  33.822  25.740   -4.446   4.359   0.435  "C3'"  ZPA  26  
ZPA  "O3'"  "O3'"  O  0  1  N  N  N   1.823  35.047  26.288   -4.809   5.688   0.059  "O3'"  ZPA  27  
ZPA  "C4'"  "C4'"  C  0  1  N  N  S  -0.192  33.849  25.633   -5.466   3.368  -0.134  "C4'"  ZPA  28  
ZPA  "O4'"  "O4'"  O  0  1  N  N  N  -0.788  34.219  26.877   -6.750   3.622   0.441  "O4'"  ZPA  29  
ZPA  "C5'"  "C5'"  C  0  1  N  N  R  -0.637  32.454  25.215   -5.026   1.942   0.206  "C5'"  ZPA  30  
ZPA  "C6'"  "C6'"  C  0  1  N  N  N  -2.144  32.374  25.211   -6.009   0.944  -0.410  "C6'"  ZPA  31  
ZPA  "O6'"  "O6'"  O  0  1  N  N  N  -2.487  33.330  24.207   -5.665  -0.380   0.003  "O6'"  ZPA  32  
ZPA  C1A    C1A    C  0  1  N  N  S  -3.891  33.484  24.062   -6.525  -1.394  -0.521  C1A    ZPA  33  
ZPA  O5A    O5A    O  0  1  N  N  N  -4.357  32.570  23.047   -7.842  -1.220   0.007  O5A    ZPA  34  
ZPA  C5A    C5A    C  0  1  N  N  N  -5.752  32.776  22.701   -8.793  -2.172  -0.475  C5A    ZPA  35  
ZPA  C4A    C4A    C  0  1  N  N  R  -5.998  34.217  22.232   -8.353  -3.581  -0.071  C4A    ZPA  36  
ZPA  O4A    O4A    O  0  1  N  N  N  -7.387  34.390  21.912   -9.272  -4.539  -0.600  O4A    ZPA  37  
ZPA  C3A    C3A    C  0  1  N  N  S  -5.551  35.191  23.322   -6.953  -3.850  -0.631  C3A    ZPA  38  
ZPA  O3A    O3A    O  0  1  N  N  N  -5.709  36.551  22.911   -6.504  -5.136  -0.197  O3A    ZPA  39  
ZPA  C2A    C2A    C  0  1  N  N  R  -4.078  34.929  23.605   -5.994  -2.772  -0.118  C2A    ZPA  40  
ZPA  O2A    O2A    O  0  1  N  N  N  -3.583  35.835  24.597   -4.700  -2.972  -0.693  O2A    ZPA  41  
ZPA  H1     H1     H  0  1  N  N  N  -1.236  31.694  16.948    8.117   1.636  -1.467  H1     ZPA  42  
ZPA  H2     H2     H  0  1  N  N  N   0.513  30.467  18.181    9.646   1.486  -3.392  H2     ZPA  43  
ZPA  H3     H3     H  0  1  N  N  N   0.314  30.135  20.621   11.650   0.061  -3.264  H3     ZPA  44  
ZPA  H4     H4     H  0  1  N  N  N  -1.652  31.032  21.829   12.123  -1.217  -1.213  H4     ZPA  45  
ZPA  H5     H5     H  0  1  N  N  N  -3.383  32.285  20.595   10.593  -1.069   0.710  H5     ZPA  46  
ZPA  H6     H6     H  0  1  N  N  N  -4.469  32.629  18.438    8.884   0.234   1.838  H6     ZPA  47  
ZPA  H7     H7     H  0  1  N  N  N  -3.552  32.405  16.909    7.849   1.362   0.929  H7     ZPA  48  
ZPA  H8     H8     H  0  1  N  N  N  -2.341  37.085  19.067    6.449  -3.567   0.411  H8     ZPA  49  
ZPA  H9     H9     H  0  1  N  N  N  -3.949  37.141  18.269    5.714  -3.008   1.946  H9     ZPA  50  
ZPA  H10    H10    H  0  1  N  N  N  -2.812  36.952  16.234    5.110  -2.106  -0.771  H10    ZPA  51  
ZPA  H11    H11    H  0  1  N  N  N  -0.443  34.404  17.621    3.457   0.623  -0.126  H11    ZPA  52  
ZPA  H12    H12    H  0  1  N  N  N   1.175  35.182  17.663    2.715  -0.763  -0.961  H12    ZPA  53  
ZPA  H13    H13    H  0  1  N  N  N   0.690  36.157  19.865    0.922  -0.835   0.750  H13    ZPA  54  
ZPA  H14    H14    H  0  1  N  N  N  -0.983  35.506  19.816    1.663   0.552   1.585  H14    ZPA  55  
ZPA  H15    H15    H  0  1  N  N  N   0.059  33.200  19.444    1.357   1.939  -0.447  H15    ZPA  56  
ZPA  H16    H16    H  0  1  N  N  N   1.646  33.949  19.828    0.616   0.553  -1.282  H16    ZPA  57  
ZPA  H17    H17    H  0  1  N  N  N  -0.763  33.934  23.079   -1.775   1.109   1.815  H17    ZPA  58  
ZPA  H18    H18    H  0  1  N  N  N   1.946  32.560  21.563   -1.154   2.610  -1.229  H18    ZPA  59  
ZPA  H19    H19    H  0  1  N  N  N   1.722  31.615  23.624   -2.667   2.457   1.294  H19    ZPA  60  
ZPA  H20    H20    H  0  1  N  N  N   1.822  34.580  23.798   -3.066   4.157  -1.211  H20    ZPA  61  
ZPA  H21    H21    H  0  1  N  N  N   3.748  33.933  24.958   -1.185   4.742   0.142  H21    ZPA  62  
ZPA  H22    H22    H  0  1  N  N  N   1.627  32.973  26.372   -4.425   4.279   1.522  H22    ZPA  63  
ZPA  H23    H23    H  0  1  N  N  N   1.465  35.172  27.159   -4.201   6.368   0.381  H23    ZPA  64  
ZPA  H24    H24    H  0  1  N  N  N  -0.480  34.564  24.848   -5.523   3.485  -1.216  H24    ZPA  65  
ZPA  H25    H25    H  0  1  N  N  N  -0.499  35.091  27.120   -7.089   4.511   0.269  H25    ZPA  66  
ZPA  H26    H26    H  0  1  N  N  N  -0.207  31.694  25.884   -5.010   1.815   1.289  H26    ZPA  67  
ZPA  H27    H27    H  0  1  N  N  N  -2.562  32.654  26.189   -7.020   1.177  -0.077  H27    ZPA  68  
ZPA  H28    H28    H  0  1  N  N  N  -2.490  31.366  24.939   -5.960   1.010  -1.497  H28    ZPA  69  
ZPA  H29    H29    H  0  1  N  N  N  -4.416  33.321  25.015   -6.556  -1.319  -1.607  H29    ZPA  70  
ZPA  H30    H30    H  0  1  N  N  N  -6.375  32.575  23.585   -9.771  -1.958  -0.043  H30    ZPA  71  
ZPA  H31    H31    H  0  1  N  N  N  -6.028  32.083  21.892   -8.854  -2.107  -1.561  H31    ZPA  72  
ZPA  H32    H32    H  0  1  N  N  N  -5.387  34.397  21.335   -8.331  -3.658   1.016  H32    ZPA  73  
ZPA  H33    H33    H  0  1  N  N  N  -7.537  35.282  21.622  -10.181  -4.425  -0.291  H33    ZPA  74  
ZPA  H34    H34    H  0  1  N  N  N  -6.132  34.997  24.235   -6.985  -3.822  -1.720  H34    ZPA  75  
ZPA  H35    H35    H  0  1  N  N  N  -5.423  37.128  23.609   -7.070  -5.867  -0.481  H35    ZPA  76  
ZPA  H36    H36    H  0  1  N  N  N  -3.517  35.069  22.669   -5.924  -2.833   0.968  H36    ZPA  77  
ZPA  H37    H37    H  0  1  N  N  N  -2.664  35.656  24.760   -4.041  -2.323  -0.411  H37    ZPA  78  
#   #
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
ZPA  O7     C7     DOUB  N  N   1  
ZPA  C7     C6     SING  N  N   2  
ZPA  C7     N8     SING  N  N   3  
ZPA  C6     S5     SING  N  N   4  
ZPA  C6     C10    SING  N  N   5  
ZPA  S5     C4     SING  N  N   6  
ZPA  N8     C11    SING  N  N   7  
ZPA  N8     C9     SING  N  N   8  
ZPA  C11    C12    SING  N  N   9  
ZPA  C4     C3     SING  N  N  10  
ZPA  C13    C12    DOUB  Y  N  11  
ZPA  C13    C14    SING  Y  N  12  
ZPA  C10    C9     SING  N  N  13  
ZPA  C12    C17    SING  Y  N  14  
ZPA  C14    C15    DOUB  Y  N  15  
ZPA  C9     O9     DOUB  N  N  16  
ZPA  C3     C2     SING  N  N  17  
ZPA  C2     C1     SING  N  N  18  
ZPA  C17    C16    DOUB  Y  N  19  
ZPA  C15    C16    SING  Y  N  20  
ZPA  C1     N1     SING  N  N  21  
ZPA  C1     N2     DOUB  N  N  22  
ZPA  O4A    C4A    SING  N  N  23  
ZPA  N1     "C1'"  SING  N  N  24  
ZPA  C4A    C5A    SING  N  N  25  
ZPA  C4A    C3A    SING  N  N  26  
ZPA  C5A    O5A    SING  N  N  27  
ZPA  O3A    C3A    SING  N  N  28  
ZPA  O5A    C1A    SING  N  N  29  
ZPA  C3A    C2A    SING  N  N  30  
ZPA  "C1'"  "O5'"  SING  N  N  31  
ZPA  "C1'"  "C2'"  SING  N  N  32  
ZPA  C2A    C1A    SING  N  N  33  
ZPA  C2A    O2A    SING  N  N  34  
ZPA  "O5'"  "C5'"  SING  N  N  35  
ZPA  C1A    "O6'"  SING  N  N  36  
ZPA  "O6'"  "C6'"  SING  N  N  37  
ZPA  "C2'"  "O2'"  SING  N  N  38  
ZPA  "C2'"  "C3'"  SING  N  N  39  
ZPA  "C6'"  "C5'"  SING  N  N  40  
ZPA  "C5'"  "C4'"  SING  N  N  41  
ZPA  "C4'"  "C3'"  SING  N  N  42  
ZPA  "C4'"  "O4'"  SING  N  N  43  
ZPA  "C3'"  "O3'"  SING  N  N  44  
ZPA  C13    H1     SING  N  N  45  
ZPA  C14    H2     SING  N  N  46  
ZPA  C15    H3     SING  N  N  47  
ZPA  C16    H4     SING  N  N  48  
ZPA  C17    H5     SING  N  N  49  
ZPA  C11    H6     SING  N  N  50  
ZPA  C11    H7     SING  N  N  51  
ZPA  C10    H8     SING  N  N  52  
ZPA  C10    H9     SING  N  N  53  
ZPA  C6     H10    SING  N  N  54  
ZPA  C4     H11    SING  N  N  55  
ZPA  C4     H12    SING  N  N  56  
ZPA  C3     H13    SING  N  N  57  
ZPA  C3     H14    SING  N  N  58  
ZPA  C2     H15    SING  N  N  59  
ZPA  C2     H16    SING  N  N  60  
ZPA  N2     H17    SING  N  N  61  
ZPA  N1     H18    SING  N  N  62  
ZPA  "C1'"  H19    SING  N  N  63  
ZPA  "C2'"  H20    SING  N  N  64  
ZPA  "O2'"  H21    SING  N  N  65  
ZPA  "C3'"  H22    SING  N  N  66  
ZPA  "O3'"  H23    SING  N  N  67  
ZPA  "C4'"  H24    SING  N  N  68  
ZPA  "O4'"  H25    SING  N  N  69  
ZPA  "C5'"  H26    SING  N  N  70  
ZPA  "C6'"  H27    SING  N  N  71  
ZPA  "C6'"  H28    SING  N  N  72  
ZPA  C1A    H29    SING  N  N  73  
ZPA  C5A    H30    SING  N  N  74  
ZPA  C5A    H31    SING  N  N  75  
ZPA  C4A    H32    SING  N  N  76  
ZPA  O4A    H33    SING  N  N  77  
ZPA  C3A    H34    SING  N  N  78  
ZPA  O3A    H35    SING  N  N  79  
ZPA  C2A    H36    SING  N  N  80  
ZPA  O2A    H37    SING  N  N  81  
#   #
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
ZPA  SMILES            ACDLabs               12.01  "O=C3N(C(=O)CC3SCCCC(=[N@H])NC2OC(COC1OCC(O)C(O)C1O)C(O)C(O)C2O)Cc4ccccc4"  
ZPA  InChI             InChI                 1.03   "InChI=1S/C26H37N3O11S/c27-17(7-4-8-41-16-9-18(31)29(25(16)37)10-13-5-2-1-3-6-13)28-24-22(35)21(34)20(33)15(40-24)12-39-26-23(36)19(32)14(30)11-38-26/h1-3,5-6,14-16,19-24,26,30,32-36H,4,7-12H2,(H2,27,28)/t14-,15-,16-,19+,20-,21+,22-,23-,24-,26+/m1/s1"  
ZPA  InChIKey          InChI                 1.03   MKGCRBLJKRCKKQ-OGJWHHEUSA-N  
ZPA  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)CCCS[C@@H]3CC(=O)N(Cc4ccccc4)C3=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O"  
ZPA  SMILES            CACTVS                3.385  "O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)CCCS[CH]3CC(=O)N(Cc4ccccc4)C3=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O"  
ZPA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "[H]/N=C(/CCCS[C@@H]1CC(=O)N(C1=O)Cc2ccccc2)\N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO[C@H]4[C@@H]([C@H]([C@@H](CO4)O)O)O)O)O)O"  
ZPA  SMILES            "OpenEye OEToolkits"  1.7.6  "c1ccc(cc1)CN2C(=O)CC(C2=O)SCCCC(=N)NC3C(C(C(C(O3)COC4C(C(C(CO4)O)O)O)O)O)O"  
#   #
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
ZPA  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-[(1Z)-4-{[(3R)-1-benzyl-2,5-dioxopyrrolidin-3-yl]sulfanyl}butanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine"  
ZPA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ZPA  "Create component"  2014-01-31  PDBJ  
ZPA  "Modify name"       2014-02-18  PDBJ  
ZPA  "Modify synonyms"   2014-02-18  PDBJ  
ZPA  "Initial release"   2014-04-23  RCSB  
ZPA  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     ZPA
_pdbx_chem_comp_synonyms.name        "4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
