data_X8Y
#

_chem_comp.id                                   X8Y
_chem_comp.name                                 "(1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H30 N6 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-06
_chem_comp.pdbx_modified_date                   2021-11-26
_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                       454.478
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    X8Y
_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       7KRY
_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
X8Y  N1   N1   N   0  1  N  N  N   -7.286  34.921  17.192   4.327  -0.220  -0.827  N1   X8Y   1  
X8Y  N3   N2   N   1  1  N  N  N  -15.548  40.049  14.697  -6.566  -2.416  -0.053  N3   X8Y   2  
X8Y  C4   C1   C   0  1  N  N  N   -7.454  34.325  15.318   6.646  -0.228  -1.615  C4   X8Y   3  
X8Y  C5   C2   C   0  1  N  N  S   -7.465  33.776  16.427   5.510  -1.067  -1.025  C5   X8Y   4  
X8Y  C6   C3   C   0  1  N  N  N   -8.259  35.828  16.607   3.096  -1.023  -0.842  C6   X8Y   5  
X8Y  C7   C4   C   0  1  N  N  N   -7.755  37.294  16.377   1.888  -0.108  -0.633  C7   X8Y   6  
X8Y  C8   C5   C   0  1  N  N  N   -9.068  38.100  16.136   0.607  -0.944  -0.649  C8   X8Y   7  
X8Y  C10  C6   C   0  1  N  N  N  -10.311  40.268  15.929  -1.883  -0.865  -0.456  C10  X8Y   8  
X8Y  C13  C7   C   0  1  Y  N  N  -15.358  40.069  16.167  -6.685  -0.942   0.016  C13  X8Y   9  
X8Y  C15  C8   C   0  1  Y  N  N  -16.350  40.162  18.385  -8.009   1.093   0.245  C15  X8Y  10  
X8Y  C17  C9   C   0  1  Y  N  N  -13.938  40.030  18.128  -5.592   1.260  -0.035  C17  X8Y  11  
X8Y  C1   C10  C   0  1  N  N  S   -5.753  33.450  13.779   7.430   0.330   0.691  C1   X8Y  12  
X8Y  C11  C11  C   0  1  N  N  N  -11.562  40.058  16.783  -3.091   0.050  -0.248  C11  X8Y  13  
X8Y  C12  C12  C   0  1  Y  N  N  -14.071  40.010  16.744  -5.530  -0.145  -0.095  C12  X8Y  14  
X8Y  C14  C13  C   0  1  Y  N  N  -16.496  40.143  16.993  -7.903  -0.379   0.178  C14  X8Y  15  
X8Y  C16  C14  C   0  1  Y  N  N  -15.072  40.104  18.949  -6.773   1.895   0.131  C16  X8Y  16  
X8Y  C18  C15  C   0  1  N  N  S   -5.930  33.122  16.549   5.952  -1.649   0.319  C18  X8Y  17  
X8Y  C19  C16  C   0  1  N  N  R   -5.119  32.722  15.146   6.295  -0.510   1.281  C19  X8Y  18  
X8Y  C2   C17  C   0  1  N  N  S   -7.167  33.920  13.757   6.989   0.912  -0.653  C2   X8Y  19  
X8Y  C3   C18  C   0  1  N  N  N   -8.055  33.699  12.786   8.124   1.752  -1.243  C3   X8Y  20  
X8Y  C9   C19  C   0  1  N  N  N   -9.103  39.586  16.602  -0.602  -0.029  -0.441  C9   X8Y  21  
X8Y  N2   N3   N   0  1  N  N  N  -12.823  39.944  15.965  -4.318  -0.750  -0.263  N2   X8Y  22  
X8Y  N4   N4   N   0  1  N  N  N  -17.519  40.238  19.275  -9.168   1.672   0.406  N4   X8Y  23  
X8Y  N5   N5   N   1  1  N  N  N  -18.418  41.349  19.196  -9.234   2.793   0.460  N5   X8Y  24  
X8Y  N6   N6   N  -1  1  N  N  N  -19.475  41.201  20.165  -9.300   3.913   0.514  N6   X8Y  25  
X8Y  O1   O1   O   0  1  N  N  N   -4.910  34.224  13.729   7.751   1.394   1.589  O1   X8Y  26  
X8Y  O2   O2   O   0  1  N  N  N   -8.273  32.307  12.859   8.524   2.744  -0.296  O2   X8Y  27  
X8Y  O3   O3   O   0  1  N  N  N   -6.815  35.184  13.449   5.838   1.736  -0.461  O3   X8Y  28  
X8Y  O4   O4   O   0  1  N  N  N  -16.810  39.734  14.181  -7.485  -3.123  -0.678  O4   X8Y  29  
X8Y  O5   O5   O  -1  1  N  N  N  -14.463  40.341  13.837  -5.540  -3.021   0.510  O5   X8Y  30  
X8Y  O6   O6   O   0  1  N  N  N   -4.744  33.482  17.375   4.891  -2.434   0.870  O6   X8Y  31  
X8Y  O7   O7   O   0  1  N  N  N   -5.649  31.824  14.921   6.707  -1.053   2.536  O7   X8Y  32  
X8Y  H1   H1   H   0  1  N  N  N   -7.484  34.748  18.157   4.401   0.311   0.027  H1   X8Y  33  
X8Y  H3   H3   H   0  1  N  N  N   -6.733  35.141  15.476   7.524  -0.856  -1.761  H3   X8Y  34  
X8Y  H4   H4   H   0  1  N  N  N   -8.471  34.740  15.261   6.331   0.187  -2.572  H4   X8Y  35  
X8Y  H5   H5   H   0  1  N  N  N   -8.258  33.073  16.722   5.266  -1.879  -1.710  H5   X8Y  36  
X8Y  H6   H6   H   0  1  N  N  N   -9.130  35.870  17.277   3.006  -1.531  -1.802  H6   X8Y  37  
X8Y  H7   H7   H   0  1  N  N  N   -8.564  35.417  15.633   3.135  -1.762  -0.042  H7   X8Y  38  
X8Y  H8   H8   H   0  1  N  N  N   -7.094  37.349  15.500   1.979   0.400   0.326  H8   X8Y  39  
X8Y  H9   H9   H   0  1  N  N  N   -7.221  37.669  17.262   1.850   0.631  -1.434  H9   X8Y  40  
X8Y  H10  H10  H   0  1  N  N  N   -9.265  38.091  15.054   0.516  -1.452  -1.609  H10  X8Y  41  
X8Y  H11  H11  H   0  1  N  N  N   -9.878  37.572  16.661   0.645  -1.683   0.151  H11  X8Y  42  
X8Y  H12  H12  H   0  1  N  N  N  -10.113  41.345  15.828  -1.844  -1.604   0.344  H12  X8Y  43  
X8Y  H13  H13  H   0  1  N  N  N  -10.470  39.830  14.933  -1.974  -1.373  -1.416  H13  X8Y  44  
X8Y  H14  H14  H   0  1  N  N  N  -12.955  39.988  18.573  -4.684   1.839  -0.119  H14  X8Y  45  
X8Y  H15  H15  H   0  1  N  N  N   -5.661  32.691  12.988   8.309  -0.299   0.544  H15  X8Y  46  
X8Y  H16  H16  H   0  1  N  N  N  -11.437  39.133  17.365  -3.001   0.558   0.712  H16  X8Y  47  
X8Y  H17  H17  H   0  1  N  N  N  -11.665  40.912  17.469  -3.130   0.789  -1.048  H17  X8Y  48  
X8Y  H18  H18  H   0  1  N  N  N  -17.481  40.185  16.553  -8.785  -0.996   0.257  H18  X8Y  49  
X8Y  H19  H19  H   0  1  N  N  N  -14.958  40.116  20.023  -6.814   2.973   0.180  H19  X8Y  50  
X8Y  H20  H20  H   0  1  N  N  N   -6.172  32.119  16.932   6.830  -2.278   0.172  H20  X8Y  51  
X8Y  H21  H21  H   0  1  N  N  N   -4.030  32.851  15.231   5.417   0.119   1.427  H21  X8Y  52  
X8Y  H22  H22  H   0  1  N  N  N   -7.646  33.983  11.805   8.972   1.106  -1.472  H22  X8Y  53  
X8Y  H23  H23  H   0  1  N  N  N   -8.987  34.254  12.970   7.780   2.238  -2.156  H23  X8Y  54  
X8Y  H24  H24  H   0  1  N  N  N   -8.174  40.093  16.303  -0.511   0.479   0.519  H24  X8Y  55  
X8Y  H25  H25  H   0  1  N  N  N   -9.210  39.632  17.696  -0.640   0.710  -1.241  H25  X8Y  56  
X8Y  H26  H26  H   0  1  N  N  N  -12.803  39.068  15.483  -4.269  -1.710  -0.393  H26  X8Y  57  
X8Y  H31  H31  H   0  1  N  N  N   -4.070  33.780  13.752   8.040   1.098   2.463  H31  X8Y  58  
X8Y  H32  H32  H   0  1  N  N  N   -8.902  32.049  12.195   9.242   3.315  -0.603  H32  X8Y  59  
X8Y  H33  H33  H   0  1  N  N  N   -6.167  35.493  14.071   5.983   2.481   0.139  H33  X8Y  60  
X8Y  H34  H34  H   0  1  N  N  N   -5.029  33.745  18.242   5.102  -2.835   1.724  H34  X8Y  61  
X8Y  H35  H35  H   0  1  N  N  N   -5.465  31.172  15.587   6.036  -1.598   2.968  H35  X8Y  62  
#   #
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
X8Y  C3   O2   SING  N  N   1  
X8Y  C3   C2   SING  N  N   2  
X8Y  O3   C2   SING  N  N   3  
X8Y  O1   C1   SING  N  N   4  
X8Y  C2   C1   SING  N  N   5  
X8Y  C2   C4   SING  N  N   6  
X8Y  C1   C19  SING  N  N   7  
X8Y  O5   N3   SING  N  N   8  
X8Y  O4   N3   DOUB  N  N   9  
X8Y  N3   C13  SING  N  N  10  
X8Y  O7   C19  SING  N  N  11  
X8Y  C19  C18  SING  N  N  12  
X8Y  C4   C5   SING  N  N  13  
X8Y  C10  C9   SING  N  N  14  
X8Y  C10  C11  SING  N  N  15  
X8Y  N2   C12  SING  N  N  16  
X8Y  N2   C11  SING  N  N  17  
X8Y  C8   C7   SING  N  N  18  
X8Y  C8   C9   SING  N  N  19  
X8Y  C13  C12  DOUB  Y  N  20  
X8Y  C13  C14  SING  Y  N  21  
X8Y  C7   C6   SING  N  N  22  
X8Y  C5   C18  SING  N  N  23  
X8Y  C5   N1   SING  N  N  24  
X8Y  C18  O6   SING  N  N  25  
X8Y  C6   N1   SING  N  N  26  
X8Y  C12  C17  SING  Y  N  27  
X8Y  C14  C15  DOUB  Y  N  28  
X8Y  C17  C16  DOUB  Y  N  29  
X8Y  C15  C16  SING  Y  N  30  
X8Y  C15  N4   SING  N  N  31  
X8Y  N5   N4   DOUB  N  N  32  
X8Y  N5   N6   DOUB  N  N  33  
X8Y  N1   H1   SING  N  N  34  
X8Y  C4   H3   SING  N  N  35  
X8Y  C4   H4   SING  N  N  36  
X8Y  C5   H5   SING  N  N  37  
X8Y  C6   H6   SING  N  N  38  
X8Y  C6   H7   SING  N  N  39  
X8Y  C7   H8   SING  N  N  40  
X8Y  C7   H9   SING  N  N  41  
X8Y  C8   H10  SING  N  N  42  
X8Y  C8   H11  SING  N  N  43  
X8Y  C10  H12  SING  N  N  44  
X8Y  C10  H13  SING  N  N  45  
X8Y  C17  H14  SING  N  N  46  
X8Y  C1   H15  SING  N  N  47  
X8Y  C11  H16  SING  N  N  48  
X8Y  C11  H17  SING  N  N  49  
X8Y  C14  H18  SING  N  N  50  
X8Y  C16  H19  SING  N  N  51  
X8Y  C18  H20  SING  N  N  52  
X8Y  C19  H21  SING  N  N  53  
X8Y  C3   H22  SING  N  N  54  
X8Y  C3   H23  SING  N  N  55  
X8Y  C9   H24  SING  N  N  56  
X8Y  C9   H25  SING  N  N  57  
X8Y  N2   H26  SING  N  N  58  
X8Y  O1   H31  SING  N  N  59  
X8Y  O2   H32  SING  N  N  60  
X8Y  O3   H33  SING  N  N  61  
X8Y  O6   H34  SING  N  N  62  
X8Y  O7   H35  SING  N  N  63  
#   #
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
X8Y  SMILES            ACDLabs               12.01  "N(C1CC(C(C(C1O)O)O)(CO)O)CCCCCCNc2c([N+](=O)[O-])cc(cc2)N=[N+]=[N-]"  
X8Y  InChI             InChI                 1.03   "InChI=1S/C19H30N6O7/c20-24-23-12-5-6-13(15(9-12)25(31)32)21-7-3-1-2-4-8-22-14-10-19(30,11-26)18(29)17(28)16(14)27/h5-6,9,14,16-18,21-22,26-30H,1-4,7-8,10-11H2/t14-,16-,17+,18-,19-/m0/s1"  
X8Y  InChIKey          InChI                 1.03   LQGVNQLERZVIBK-UJCHZGTJSA-N  
X8Y  SMILES_CANONICAL  CACTVS                3.385  "OC[C@@]1(O)C[C@H](NCCCCCCNc2ccc(cc2[N+]([O-])=O)N=[N+]=[N-])[C@H](O)[C@@H](O)[C@@H]1O"  
X8Y  SMILES            CACTVS                3.385  "OC[C]1(O)C[CH](NCCCCCCNc2ccc(cc2[N+]([O-])=O)N=[N+]=[N-])[CH](O)[CH](O)[CH]1O"  
X8Y  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCCCCCN[C@H]2C[C@@]([C@H]([C@@H]([C@H]2O)O)O)(CO)O"  
X8Y  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCCCCCNC2CC(C(C(C2O)O)O)(CO)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
X8Y  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol"  
X8Y  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(1~{S},2~{S},3~{R},4~{S},5~{S})-5-[6-[(4-azido-2-nitro-phenyl)amino]hexylamino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
X8Y  "Create component"  2020-12-06  RCSB  
X8Y  "Initial release"   2021-12-01  RCSB  
##
