data_CK0
#

_chem_comp.id                                   CK0
_chem_comp.name                                 "(2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S,6R)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H36 N4 O11"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        '3"-deamino-3"-hydroxykanamycin B'
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-04-25
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       484.499
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    CK0
_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       6JW8
_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
CK0  C4   C1   C  0  1  N  N  S  47.993  3.457   1.105  -4.817   1.666   0.370  C4   CK0   1  
CK0  C5   C2   C  0  1  N  N  R  49.018  3.720  -0.050  -3.480   1.324   1.032  C5   CK0   2  
CK0  C6   C3   C  0  1  N  N  N  50.187  2.755  -0.164  -3.274   2.216   2.258  C6   CK0   3  
CK0  C3   C4   C  0  1  N  N  S  46.818  4.418   0.828  -5.045   0.729  -0.820  C3   CK0   4  
CK0  O2   O1   O  0  1  N  N  N  45.236  5.077  -0.932  -5.134  -1.606  -1.444  O2   CK0   5  
CK0  C2   C5   C  0  1  N  N  R  46.243  4.175  -0.608  -4.994  -0.721  -0.331  C2   CK0   6  
CK0  O3   O2   O  0  1  N  N  N  45.724  4.275   1.712  -6.325   0.994  -1.398  O3   CK0   7  
CK0  O4   O3   O  0  1  N  N  N  48.627  3.694   2.424  -4.791   3.020  -0.087  O4   CK0   8  
CK0  O6   O4   O  0  1  N  N  N  49.531  1.487  -0.136  -1.977   1.977   2.808  O6   CK0   9  
CK0  O5   O5   O  0  1  N  N  N  48.443  3.451  -1.336  -3.488  -0.047   1.436  O5   CK0  10  
CK0  C1   C6   C  0  1  N  N  S  47.330  4.252  -1.696  -3.650  -0.973   0.357  C1   CK0  11  
CK0  O1   O6   O  0  1  N  N  N  47.761  5.593  -1.828  -2.591  -0.795  -0.586  O1   CK0  12  
CK0  CBG  C7   C  0  1  N  N  S  48.128  5.953  -3.110  -1.324  -1.277  -0.135  CBG  CK0  13  
CK0  CBA  C8   C  0  1  N  N  S  49.575  6.462  -2.991  -0.207  -0.436  -0.757  CBA  CK0  14  
CK0  OAK  O7   O  0  1  N  N  N  50.446  5.439  -2.532  -0.365   0.930  -0.365  OAK  CK0  15  
CK0  CAT  C9   C  0  1  N  N  R  47.194  7.061  -3.610  -1.155  -2.739  -0.554  CAT  CK0  16  
CK0  NAC  N1   N  0  1  N  N  N  45.740  6.700  -3.570  -2.227  -3.546   0.044  NAC  CK0  17  
CK0  CAN  C10  C  0  1  N  N  N  47.620  7.375  -4.992   0.202  -3.254  -0.070  CAN  CK0  18  
CK0  CAS  C11  C  0  1  N  N  S  48.929  8.074  -4.906   1.319  -2.413  -0.692  CAS  CK0  19  
CK0  NAB  N2   N  0  1  N  N  N  49.256  8.611  -6.221   2.622  -2.908  -0.228  NAB  CK0  20  
CK0  CBF  C12  C  0  1  N  N  R  49.981  6.995  -4.403   1.150  -0.951  -0.273  CBF  CK0  21  
CK0  OAQ  O8   O  0  1  N  N  N  51.268  7.548  -4.282   2.193  -0.166  -0.854  OAQ  CK0  22  
CK0  CBD  C13  C  0  1  N  N  R  52.443  6.671  -4.424   2.502   1.022  -0.122  CBD  CK0  23  
CK0  OAO  O9   O  0  1  N  N  N  52.478  6.213  -5.800   3.188   0.674   1.082  OAO  CK0  24  
CK0  CBB  C14  C  0  1  N  N  R  52.507  7.429  -6.660   4.404  -0.046   0.873  CBB  CK0  25  
CK0  CAL  C15  C  0  1  N  N  N  52.235  7.027  -8.093   5.034  -0.387   2.226  CAL  CK0  26  
CK0  NAA  N3   N  0  1  N  N  N  53.222  5.965  -8.373   4.156  -1.312   2.955  NAA  CK0  27  
CK0  CAX  C16  C  0  1  N  N  S  53.849  8.168  -6.430   5.374   0.817   0.062  CAX  CK0  28  
CK0  OAH  O10  O  0  1  N  N  N  54.071  9.307  -7.246   6.569   0.077  -0.197  OAH  CK0  29  
CK0  CAV  C17  C  0  1  N  N  R  53.718  8.721  -5.073   4.714   1.204  -1.264  CAV  CK0  30  
CK0  OAF  O11  O  0  1  N  N  N  54.807  9.588  -4.857   5.583   2.070  -1.996  OAF  CK0  31  
CK0  CAU  C18  C  0  1  N  N  R  53.654  7.560  -4.082   3.396   1.928  -0.974  CAU  CK0  32  
CK0  NAD  N4   N  0  1  N  N  N  53.472  8.115  -2.752   2.717   2.238  -2.239  NAD  CK0  33  
CK0  H1   H1   H  0  1  N  N  N  47.637  2.418   1.038  -5.624   1.541   1.092  H1   CK0  34  
CK0  H2   H2   H  0  1  N  N  N  49.387  4.754   0.015  -2.670   1.489   0.322  H2   CK0  35  
CK0  H3   H3   H  0  1  N  N  N  50.880  2.865   0.683  -3.357   3.262   1.964  H3   CK0  36  
CK0  H4   H4   H  0  1  N  N  N  50.735  2.901  -1.107  -4.034   1.987   3.005  H4   CK0  37  
CK0  H5   H5   H  0  1  N  N  N  47.201  5.449   0.869  -4.268   0.891  -1.566  H5   CK0  38  
CK0  H6   H6   H  0  1  N  N  N  44.555  5.043  -0.270  -5.110  -2.543  -1.207  H6   CK0  39  
CK0  H7   H7   H  0  1  N  N  N  45.835  3.154  -0.624  -5.805  -0.896   0.377  H7   CK0  40  
CK0  H8   H8   H  0  1  N  N  N  46.018  4.413   2.605  -6.536   0.435  -2.159  H8   CK0  41  
CK0  H9   H9   H  0  1  N  N  N  47.994  3.531   3.114  -5.607   3.305  -0.520  H9   CK0  42  
CK0  H10  H10  H  0  1  N  N  N  50.177  0.794  -0.202  -1.777   2.510   3.590  H10  CK0  43  
CK0  H11  H11  H  0  1  N  N  N  46.900  3.897  -2.644  -3.625  -1.991   0.745  H11  CK0  44  
CK0  H12  H12  H  0  1  N  N  N  48.093  5.099  -3.802  -1.273  -1.202   0.952  H12  CK0  45  
CK0  H13  H13  H  0  1  N  N  N  49.588  7.309  -2.290  -0.258  -0.510  -1.843  H13  CK0  46  
CK0  H14  H14  H  0  1  N  N  N  50.165  5.144  -1.674  -1.156   1.353  -0.726  H14  CK0  47  
CK0  H15  H15  H  0  1  N  N  N  47.351  7.950  -2.981  -1.206  -2.813  -1.640  H15  CK0  48  
CK0  H16  H16  H  0  1  N  N  N  45.473  6.492  -2.629  -2.137  -4.516  -0.219  H16  CK0  49  
CK0  H17  H17  H  0  1  N  N  N  45.196  7.468  -3.908  -2.241  -3.443   1.047  H17  CK0  50  
CK0  H19  H19  H  0  1  N  N  N  46.877  8.026  -5.476   0.253  -3.180   1.016  H19  CK0  51  
CK0  H20  H20  H  0  1  N  N  N  47.727  6.447  -5.572   0.323  -4.296  -0.369  H20  CK0  52  
CK0  H21  H21  H  0  1  N  N  N  48.874  8.884  -4.164   1.268  -2.488  -1.779  H21  CK0  53  
CK0  H22  H22  H  0  1  N  N  N  50.136  9.085  -6.179   2.760  -3.870  -0.500  H22  CK0  54  
CK0  H23  H23  H  0  1  N  N  N  49.312  7.863  -6.882   3.372  -2.325  -0.567  H23  CK0  55  
CK0  H25  H25  H  0  1  N  N  N  49.981  6.153  -5.111   1.201  -0.877   0.813  H25  CK0  56  
CK0  H26  H26  H  0  1  N  N  N  52.389  5.825  -3.723   1.580   1.548   0.123  H26  CK0  57  
CK0  H27  H27  H  0  1  N  N  N  51.698  8.101  -6.336   4.193  -0.966   0.328  H27  CK0  58  
CK0  H28  H28  H  0  1  N  N  N  52.380  7.881  -8.771   6.004  -0.857   2.067  H28  CK0  59  
CK0  H29  H29  H  0  1  N  N  N  51.210  6.643  -8.201   5.162   0.526   2.807  H29  CK0  60  
CK0  H30  H30  H  0  1  N  N  N  53.107  5.642  -9.312   3.968  -2.139   2.408  H30  CK0  61  
CK0  H31  H31  H  0  1  N  N  N  54.146  6.330  -8.257   4.549  -1.553   3.852  H31  CK0  62  
CK0  H33  H33  H  0  1  N  N  N  54.684  7.455  -6.487   5.618   1.718   0.625  H33  CK0  63  
CK0  H34  H34  H  0  1  N  N  N  54.914  9.690  -7.033   7.230   0.564  -0.708  H34  CK0  64  
CK0  H35  H35  H  0  1  N  N  N  52.775  9.283  -5.006   4.517   0.306  -1.849  H35  CK0  65  
CK0  H36  H36  H  0  1  N  N  N  54.748  9.961  -3.985   6.441   1.678  -2.209  H36  CK0  66  
CK0  H37  H37  H  0  1  N  N  N  54.579  6.967  -4.139   3.599   2.852  -0.432  H37  CK0  67  
CK0  H38  H38  H  0  1  N  N  N  53.427  7.372  -2.084   1.841   2.712  -2.073  H38  CK0  68  
CK0  H39  H39  H  0  1  N  N  N  54.242  8.714  -2.533   3.312   2.782  -2.845  H39  CK0  69  
#   #
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
CK0  NAA  CAL  SING  N  N   1  
CK0  CAL  CBB  SING  N  N   2  
CK0  OAH  CAX  SING  N  N   3  
CK0  CBB  CAX  SING  N  N   4  
CK0  CBB  OAO  SING  N  N   5  
CK0  CAX  CAV  SING  N  N   6  
CK0  NAB  CAS  SING  N  N   7  
CK0  OAO  CBD  SING  N  N   8  
CK0  CAV  OAF  SING  N  N   9  
CK0  CAV  CAU  SING  N  N  10  
CK0  CAN  CAS  SING  N  N  11  
CK0  CAN  CAT  SING  N  N  12  
CK0  CAS  CBF  SING  N  N  13  
CK0  CBD  OAQ  SING  N  N  14  
CK0  CBD  CAU  SING  N  N  15  
CK0  CBF  OAQ  SING  N  N  16  
CK0  CBF  CBA  SING  N  N  17  
CK0  CAU  NAD  SING  N  N  18  
CK0  CAT  NAC  SING  N  N  19  
CK0  CAT  CBG  SING  N  N  20  
CK0  CBG  CBA  SING  N  N  21  
CK0  CBG  O1   SING  N  N  22  
CK0  CBA  OAK  SING  N  N  23  
CK0  O1   C1   SING  N  N  24  
CK0  C1   O5   SING  N  N  25  
CK0  C1   C2   SING  N  N  26  
CK0  O5   C5   SING  N  N  27  
CK0  O2   C2   SING  N  N  28  
CK0  C2   C3   SING  N  N  29  
CK0  C6   O6   SING  N  N  30  
CK0  C6   C5   SING  N  N  31  
CK0  C5   C4   SING  N  N  32  
CK0  C3   C4   SING  N  N  33  
CK0  C3   O3   SING  N  N  34  
CK0  C4   O4   SING  N  N  35  
CK0  C4   H1   SING  N  N  36  
CK0  C5   H2   SING  N  N  37  
CK0  C6   H3   SING  N  N  38  
CK0  C6   H4   SING  N  N  39  
CK0  C3   H5   SING  N  N  40  
CK0  O2   H6   SING  N  N  41  
CK0  C2   H7   SING  N  N  42  
CK0  O3   H8   SING  N  N  43  
CK0  O4   H9   SING  N  N  44  
CK0  O6   H10  SING  N  N  45  
CK0  C1   H11  SING  N  N  46  
CK0  CBG  H12  SING  N  N  47  
CK0  CBA  H13  SING  N  N  48  
CK0  OAK  H14  SING  N  N  49  
CK0  CAT  H15  SING  N  N  50  
CK0  NAC  H16  SING  N  N  51  
CK0  NAC  H17  SING  N  N  52  
CK0  CAN  H19  SING  N  N  53  
CK0  CAN  H20  SING  N  N  54  
CK0  CAS  H21  SING  N  N  55  
CK0  NAB  H22  SING  N  N  56  
CK0  NAB  H23  SING  N  N  57  
CK0  CBF  H25  SING  N  N  58  
CK0  CBD  H26  SING  N  N  59  
CK0  CBB  H27  SING  N  N  60  
CK0  CAL  H28  SING  N  N  61  
CK0  CAL  H29  SING  N  N  62  
CK0  NAA  H30  SING  N  N  63  
CK0  NAA  H31  SING  N  N  64  
CK0  CAX  H33  SING  N  N  65  
CK0  OAH  H34  SING  N  N  66  
CK0  CAV  H35  SING  N  N  67  
CK0  OAF  H36  SING  N  N  68  
CK0  CAU  H37  SING  N  N  69  
CK0  NAD  H38  SING  N  N  70  
CK0  NAD  H39  SING  N  N  71  
#   #
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
CK0  InChI             InChI                 1.03   "InChI=1S/C18H36N4O11/c19-2-6-9(24)11(26)8(22)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)12(27)10(25)7(3-23)31-18/h4-18,23-29H,1-3,19-22H2/t4-,5+,6+,7+,8+,9+,10+,11+,12-,13+,14-,15+,16-,17+,18+/m0/s1"  
CK0  InChIKey          InChI                 1.03   MOWMHIINUAQFMU-DNBVWFFRSA-N  
CK0  SMILES_CANONICAL  CACTVS                3.385  "NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1O"  
CK0  SMILES            CACTVS                3.385  "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)[CH]2O)[CH](N)[CH](O)[CH]1O"  
CK0  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N"  
CK0  SMILES            "OpenEye OEToolkits"  2.0.6  "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)O)O)O)OC3C(C(C(C(O3)CN)O)O)N)N"  
#
_pdbx_chem_comp_identifier.comp_id          CK0
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CK0  "Create component"  2019-04-25  PDBJ  
CK0  "Initial release"   2020-04-15  RCSB  
CK0  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     CK0
_pdbx_chem_comp_synonyms.name        '3"-deamino-3"-hydroxykanamycin B'
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
