data_CD7
#

_chem_comp.id                                   CD7
_chem_comp.name                                 "(2S,5Z)-1-formyl-5-imino-N'-[(3R)-1-(sulfooxy)pyrrolidine-3-carbonyl]piperidine-2-carbohydrazide"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C12 H19 N5 O7 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "open form - WCK 5153"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-09-20
_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                       377.374
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    CD7
_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       6B1Y
_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
CD7  OAB  O1   O  0  1  N  N  N   8.877   1.128  -2.180  -4.309  -3.095  -0.569  OAB  CD7   1  
CD7  CAE  C1   C  0  1  N  N  N   9.148   0.075  -2.771  -3.841  -1.991  -0.387  CAE  CD7   2  
CD7  N    N1   N  0  1  N  N  N  10.406  -0.334  -3.016  -4.620  -0.899  -0.517  N    CD7   3  
CD7  CAL  C2   C  0  1  N  N  N  10.650  -1.685  -3.577  -6.010  -1.019  -0.987  CAL  CD7   4  
CD7  CAP  C3   C  0  1  N  N  N  11.614  -2.230  -2.640  -6.886  -0.232  -0.035  CAP  CD7   5  
CD7  NAA  N2   N  0  1  N  N  N  11.649  -3.526  -2.404  -7.976  -0.725   0.419  NAA  CD7   6  
CD7  CAH  C4   C  0  1  N  N  N  12.549  -1.498  -1.876  -6.433   1.156   0.363  CAH  CD7   7  
CD7  CB   C5   C  0  1  N  N  N  12.152  -0.118  -1.575  -4.994   1.072   0.884  CB   CD7   8  
CD7  CA   C6   C  0  1  N  N  S  11.509   0.587  -2.783  -4.103   0.435  -0.186  CA   CD7   9  
CD7  C    C7   C  0  1  N  N  N  12.365   0.850  -3.913  -2.698   0.312   0.345  C    CD7  10  
CD7  O    O2   O  0  1  N  N  N  11.966   0.656  -5.076  -2.442  -0.511   1.199  O    CD7  11  
CD7  NAO  N3   N  0  1  N  N  N  13.600   1.368  -3.615  -1.726   1.117  -0.128  NAO  CD7  12  
CD7  NAN  N4   N  0  1  N  N  N  14.310   1.905  -4.604  -0.420   1.003   0.366  NAN  CD7  13  
CD7  CAQ  C8   C  0  1  N  N  N  14.031   3.167  -4.988   0.552   1.808  -0.107  CAQ  CD7  14  
CD7  OAC  O3   O  0  1  N  N  N  13.016   3.739  -4.633   0.296   2.631  -0.960  OAC  CD7  15  
CD7  CAS  C9   C  0  1  N  N  R  15.083   3.830  -5.911   1.957   1.686   0.424  CAS  CD7  16  
CD7  CAI  C10  C  0  1  N  N  N  16.318   4.157  -5.177   2.893   2.706  -0.263  CAI  CD7  17  
CD7  CAF  C11  C  0  1  N  N  N  15.805   5.437  -4.358   4.214   1.949  -0.493  CAF  CD7  18  
CD7  NAM  N5   N  0  1  N  N  N  14.712   6.061  -5.205   4.038   0.590   0.063  NAM  CD7  19  
CD7  CAK  C12  C  0  1  N  N  N  14.645   5.209  -6.409   2.577   0.323   0.025  CAK  CD7  20  
CD7  H1   H1   H  0  1  N  Y  N   8.332  -0.548  -3.107  -2.801  -1.884  -0.116  H1   CD7  21  
CD7  H2   H2   H  0  1  N  N  N   9.727  -2.283  -3.595  -6.096  -0.608  -1.994  H2   CD7  22  
CD7  H3   H3   H  0  1  N  N  N  11.068  -1.627  -4.593  -6.311  -2.066  -0.988  H3   CD7  23  
CD7  H4   H4   H  0  1  N  N  N  12.338  -3.764  -1.719  -8.526  -0.208   1.029  H4   CD7  24  
CD7  H5   H5   H  0  1  N  N  N  12.700  -2.026  -0.923  -6.471   1.816  -0.503  H5   CD7  25  
CD7  H6   H6   H  0  1  N  N  N  13.497  -1.468  -2.433  -7.084   1.542   1.148  H6   CD7  26  
CD7  H7   H7   H  0  1  N  N  N  13.045   0.448  -1.271  -4.630   2.074   1.111  H7   CD7  27  
CD7  H8   H8   H  0  1  N  N  N  11.427  -0.132  -0.748  -4.970   0.463   1.787  H8   CD7  28  
CD7  H9   H9   H  0  1  N  N  N  11.096   1.542  -2.425  -4.101   1.057  -1.081  H9   CD7  29  
CD7  H10  H10  H  0  1  N  N  N  13.956   1.343  -2.681  -1.931   1.776  -0.810  H10  CD7  30  
CD7  H11  H11  H  0  1  N  N  N  15.035   1.383  -5.053  -0.215   0.345   1.048  H11  CD7  31  
CD7  H12  H12  H  0  1  N  N  N  15.298   3.171  -6.765   1.972   1.817   1.506  H12  CD7  32  
CD7  H13  H13  H  0  1  N  N  N  16.628   3.339  -4.510   2.470   3.026  -1.215  H13  CD7  33  
CD7  H14  H14  H  0  1  N  N  N  17.145   4.409  -5.857   3.057   3.566   0.386  H14  CD7  34  
CD7  H15  H15  H  0  1  N  N  N  16.628   6.151  -4.209   4.426   1.889  -1.561  H15  CD7  35  
CD7  H16  H16  H  0  1  N  N  N  15.404   5.130  -3.381   5.029   2.461   0.019  H16  CD7  36  
CD7  O1   O4   O  0  1  N  N  N  13.821   6.068  -4.709   4.773  -0.399  -0.726  O1   CD7  37  
CD7  H19  H19  H  0  1  N  N  N  15.328   5.579  -7.188   2.308  -0.448   0.746  H19  CD7  38  
CD7  H20  H20  H  0  1  N  N  N  13.620   5.174  -6.807   2.265   0.038  -0.980  H20  CD7  39  
CD7  S1   S1   S  0  1  N  N  N       ?       ?       ?   5.830  -1.158   0.063  S1   CD7  40  
CD7  O3   O5   O  0  1  N  N  N       ?       ?       ?   6.570  -1.916  -0.885  O3   CD7  41  
CD7  O2   O6   O  0  1  N  N  N       ?       ?       ?   6.428  -0.216   0.942  O2   CD7  42  
CD7  O4   O7   O  0  1  N  N  N       ?       ?       ?   5.101  -2.164   0.942  O4   CD7  43  
CD7  H17  H17  H  0  1  N  N  N       ?       ?       ?   5.686  -2.704   1.490  H17  CD7  44  
#   #
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
CD7  CAK  CAS  SING  N  N   1  
CD7  CAK  NAM  SING  N  N   2  
CD7  CAS  CAI  SING  N  N   3  
CD7  CAS  CAQ  SING  N  N   4  
CD7  NAM  CAF  SING  N  N   5  
CD7  CAI  CAF  SING  N  N   6  
CD7  O    C    DOUB  N  N   7  
CD7  CAQ  OAC  DOUB  N  N   8  
CD7  CAQ  NAN  SING  N  N   9  
CD7  NAN  NAO  SING  N  N  10  
CD7  C    NAO  SING  N  N  11  
CD7  C    CA   SING  N  N  12  
CD7  CAL  N    SING  N  N  13  
CD7  CAL  CAP  SING  N  N  14  
CD7  N    CA   SING  N  N  15  
CD7  N    CAE  SING  N  N  16  
CD7  CA   CB   SING  N  N  17  
CD7  CAE  OAB  DOUB  N  N  18  
CD7  CAP  NAA  DOUB  N  N  19  
CD7  CAP  CAH  SING  N  N  20  
CD7  CAH  CB   SING  N  N  21  
CD7  CAE  H1   SING  N  N  22  
CD7  CAL  H2   SING  N  N  23  
CD7  CAL  H3   SING  N  N  24  
CD7  NAA  H4   SING  N  N  25  
CD7  CAH  H5   SING  N  N  26  
CD7  CAH  H6   SING  N  N  27  
CD7  CB   H7   SING  N  N  28  
CD7  CB   H8   SING  N  N  29  
CD7  CA   H9   SING  N  N  30  
CD7  NAO  H10  SING  N  N  31  
CD7  NAN  H11  SING  N  N  32  
CD7  CAS  H12  SING  N  N  33  
CD7  CAI  H13  SING  N  N  34  
CD7  CAI  H14  SING  N  N  35  
CD7  CAF  H15  SING  N  N  36  
CD7  CAF  H16  SING  N  N  37  
CD7  NAM  O1   SING  N  N  38  
CD7  CAK  H19  SING  N  N  39  
CD7  CAK  H20  SING  N  N  40  
CD7  O1   S1   SING  N  N  41  
CD7  S1   O3   DOUB  N  N  42  
CD7  S1   O2   DOUB  N  N  43  
CD7  S1   O4   SING  N  N  44  
CD7  O4   H17  SING  N  N  45  
#   #
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
CD7  SMILES            ACDLabs               12.01  "O=CN1C(CCC(/C1)=N)C(NNC(=O)C2CCN(OS(=O)(=O)O)C2)=O"  
CD7  InChI             InChI                 1.03   "InChI=1S/C12H19N5O7S/c13-9-1-2-10(16(6-9)7-18)12(20)15-14-11(19)8-3-4-17(5-8)24-25(21,22)23/h7-8,10,13H,1-6H2,(H,14,19)(H,15,20)(H,21,22,23)/b13-9-/t8-,10+/m1/s1"  
CD7  InChIKey          InChI                 1.03   APRDZKRWJZJQAT-NBGMFQDKSA-N  
CD7  SMILES_CANONICAL  CACTVS                3.385  "O[S](=O)(=O)ON1CC[C@H](C1)C(=O)NNC(=O)[C@@H]2CCC(=N)CN2C=O"  
CD7  SMILES            CACTVS                3.385  "O[S](=O)(=O)ON1CC[CH](C1)C(=O)NNC(=O)[CH]2CCC(=N)CN2C=O"  
CD7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "[H]/N=C\1/CC[C@H](N(C1)C=O)C(=O)NNC(=O)[C@@H]2CCN(C2)OS(=O)(=O)O"  
CD7  SMILES            "OpenEye OEToolkits"  2.0.6  "C1CC(=N)CN(C1C(=O)NNC(=O)C2CCN(C2)OS(=O)(=O)O)C=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
CD7  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S,5Z)-1-formyl-5-imino-N'-[(3R)-1-(sulfooxy)pyrrolidine-3-carbonyl]piperidine-2-carbohydrazide"  
CD7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(3~{R})-3-[[[(2~{S})-5-azanylidene-1-methanoyl-piperidin-2-yl]carbonylamino]carbamoyl]pyrrolidin-1-yl] hydrogen sulfate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CD7  "Create component"  2017-09-20  RCSB  
CD7  "Initial release"   2018-08-01  RCSB  
CD7  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     CD7
_pdbx_chem_comp_synonyms.name        "open form - WCK 5153"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
