data_SY5
#

_chem_comp.id                                   SY5
_chem_comp.name                                 "2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C12 H27 N5 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "N6-(3-aminopropyl)-negamycin"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-03
_chem_comp.pdbx_modified_date                   2021-05-21
_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                       305.374
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    SY5
_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       7B5K
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
SY5  C09   C1   C  0  1  N  N  R  191.632  104.451  176.590  -0.314  -0.588  -0.059  C09   SY5   1  
SY5  C10   C2   C  0  1  N  N  N  190.476  103.527  176.151   0.956  -0.505   0.789  C10   SY5   2  
SY5  C11   C3   C  0  1  N  N  R  190.026  103.649  174.672   2.156  -0.219  -0.117  C11   SY5   3  
SY5  C12   C4   C  0  1  N  N  N  192.973  104.042  175.972  -1.529  -0.750   0.858  C12   SY5   4  
SY5  C13   C5   C  0  1  N  N  N  189.757  102.272  174.026   3.442  -0.258   0.712  C13   SY5   5  
SY5  C14   C6   C  0  1  N  N  N  194.070  104.323  177.027  -2.789  -0.709   0.033  C14   SY5   6  
SY5  C15   C7   C  0  1  N  N  N  195.541  103.495  179.835  -6.001   0.314   0.302  C15   SY5   7  
SY5  C16   C8   C  0  1  N  N  N  196.875  104.616  178.151  -5.848  -2.077  -0.049  C16   SY5   8  
SY5  C17   C9   C  0  1  N  N  N  194.169  102.900  179.979  -5.314   1.624   0.013  C17   SY5   9  
SY5  C18   C10  C  0  1  N  N  N  188.585  101.516  172.113   5.848  -0.014   0.605  C18   SY5  10  
SY5  C19   C11  C  0  1  N  N  N  187.264  100.783  171.856   7.022   0.276  -0.332  C19   SY5  11  
SY5  C20   C12  C  0  1  N  N  N  187.530   99.244  171.744   8.329   0.245   0.463  C20   SY5  12  
SY5  N05   N1   N  0  1  N  N  N  191.779  104.306  178.001  -0.225  -1.743  -0.962  N05   SY5  13  
SY5  N06   N2   N  0  1  N  N  N  194.997  103.248  177.460  -3.991  -0.833   0.631  N06   SY5  14  
SY5  N07   N3   N  0  1  N  N  N  196.027  103.465  178.453  -5.133  -0.796  -0.117  N07   SY5  15  
SY5  N08   N4   N  0  1  N  N  N  188.461  102.201  173.398   4.593   0.016  -0.158  N08   SY5  16  
SY5  N21   N5   N  0  1  N  N  N  186.253   98.545  171.726   9.456   0.523  -0.438  N21   SY5  17  
SY5  O01   O1   O  0  1  N  N  N  190.976  104.269  173.903   2.009   1.074  -0.707  O01   SY5  18  
SY5  O02   O2   O  0  1  N  N  N  194.107  105.403  177.478  -2.723  -0.565  -1.170  O02   SY5  19  
SY5  O03   O3   O  0  1  N  N  N  193.171  103.566  179.619  -4.216   1.633  -0.489  O03   SY5  20  
SY5  O04   O4   O  0  1  N  N  N  194.024  101.749  180.469  -5.924   2.781   0.315  O04   SY5  21  
SY5  H091  H1   H  0  0  N  N  N  191.398  105.491  176.317  -0.421   0.324  -0.645  H091  SY5  22  
SY5  H102  H2   H  0  0  N  N  N  189.607  103.752  176.786   0.854   0.298   1.520  H102  SY5  23  
SY5  H101  H3   H  0  0  N  N  N  190.794  102.488  176.320   1.110  -1.451   1.308  H101  SY5  24  
SY5  H111  H4   H  0  0  N  N  N  189.087  104.221  174.652   2.206  -0.973  -0.902  H111  SY5  25  
SY5  H122  H5   H  0  0  N  N  N  192.960  102.972  175.718  -1.467  -1.705   1.379  H122  SY5  26  
SY5  H121  H6   H  0  0  N  N  N  193.164  104.632  175.063  -1.545   0.061   1.586  H121  SY5  27  
SY5  H132  H7   H  0  0  N  N  N  189.814  101.499  174.807   3.391   0.496   1.497  H132  SY5  28  
SY5  H131  H8   H  0  0  N  N  N  190.529  102.082  173.265   3.553  -1.245   1.162  H131  SY5  29  
SY5  H152  H9   H  0  0  N  N  N  196.240  102.926  180.466  -6.200   0.235   1.370  H152  SY5  30  
SY5  H151  H10  H  0  0  N  N  N  195.509  104.541  180.174  -6.941   0.267  -0.248  H151  SY5  31  
SY5  H162  H11  H  0  0  N  N  N  197.635  104.729  178.938  -6.115  -2.291   0.986  H162  SY5  32  
SY5  H163  H12  H  0  0  N  N  N  197.371  104.461  177.182  -6.754  -2.020  -0.653  H163  SY5  33  
SY5  H161  H13  H  0  0  N  N  N  196.257  105.525  178.105  -5.207  -2.872  -0.431  H161  SY5  34  
SY5  H1    H14  H  0  1  N  N  N  189.415  100.794  172.150   5.977  -0.998   1.055  H1    SY5  35  
SY5  H2    H15  H  0  1  N  N  N  188.771  102.248  171.313   5.814   0.742   1.390  H2    SY5  36  
SY5  H3    H16  H  0  1  N  N  N  186.820  101.147  170.918   7.056  -0.480  -1.117  H3    SY5  37  
SY5  H4    H17  H  0  1  N  N  N  186.571  100.975  172.688   6.894   1.261  -0.782  H4    SY5  38  
SY5  H5    H18  H  0  1  N  N  N  188.123   98.908  172.607   8.295   1.001   1.247  H5    SY5  39  
SY5  H6    H19  H  0  1  N  N  N  188.081   99.031  170.816   8.458  -0.740   0.912  H6    SY5  40  
SY5  H7    H20  H  0  1  N  N  N  190.925  104.562  178.454   0.531  -1.630  -1.620  H7    SY5  41  
SY5  H051  H21  H  0  0  N  N  N  191.998  103.355  178.217  -0.126  -2.602  -0.442  H051  SY5  42  
SY5  H061  H23  H  0  0  N  N  N  194.907  102.340  177.050  -4.044  -0.948   1.593  H061  SY5  43  
SY5  H081  H24  H  0  0  N  N  N  188.110  103.126  173.251   4.482   0.897  -0.637  H081  SY5  44  
SY5  H9    H26  H  0  1  N  N  N  186.412   97.560  171.655   9.329   1.402  -0.916  H9    SY5  45  
SY5  H10   H27  H  0  1  N  N  N  185.754   98.741  172.570  10.332   0.508   0.064  H10   SY5  46  
SY5  H011  H29  H  0  0  N  N  N  191.171  105.124  174.268   1.958   1.796  -0.065  H011  SY5  47  
SY5  H12   H30  H  0  1  N  N  N  193.100  101.531  180.498  -5.445   3.596   0.111  H12   SY5  48  
#   #
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
SY5  N21  C20   SING  N  N   1  
SY5  C20  C19   SING  N  N   2  
SY5  C19  C18   SING  N  N   3  
SY5  C18  N08   SING  N  N   4  
SY5  N08  C13   SING  N  N   5  
SY5  O01  C11   SING  N  N   6  
SY5  C13  C11   SING  N  N   7  
SY5  C11  C10   SING  N  N   8  
SY5  C12  C09   SING  N  N   9  
SY5  C12  C14   SING  N  N  10  
SY5  C10  C09   SING  N  N  11  
SY5  C09  N05   SING  N  N  12  
SY5  C14  N06   SING  N  N  13  
SY5  C14  O02   DOUB  N  N  14  
SY5  N06  N07   SING  N  N  15  
SY5  C16  N07   SING  N  N  16  
SY5  N07  C15   SING  N  N  17  
SY5  O03  C17   DOUB  N  N  18  
SY5  C15  C17   SING  N  N  19  
SY5  C17  O04   SING  N  N  20  
SY5  C09  H091  SING  N  N  21  
SY5  C10  H102  SING  N  N  22  
SY5  C10  H101  SING  N  N  23  
SY5  C11  H111  SING  N  N  24  
SY5  C12  H122  SING  N  N  25  
SY5  C12  H121  SING  N  N  26  
SY5  C13  H132  SING  N  N  27  
SY5  C13  H131  SING  N  N  28  
SY5  C15  H152  SING  N  N  29  
SY5  C15  H151  SING  N  N  30  
SY5  C16  H162  SING  N  N  31  
SY5  C16  H163  SING  N  N  32  
SY5  C16  H161  SING  N  N  33  
SY5  C18  H1    SING  N  N  34  
SY5  C18  H2    SING  N  N  35  
SY5  C19  H3    SING  N  N  36  
SY5  C19  H4    SING  N  N  37  
SY5  C20  H5    SING  N  N  38  
SY5  C20  H6    SING  N  N  39  
SY5  N05  H7    SING  N  N  40  
SY5  N05  H051  SING  N  N  41  
SY5  N06  H061  SING  N  N  42  
SY5  N08  H081  SING  N  N  43  
SY5  N21  H9    SING  N  N  44  
SY5  N21  H10   SING  N  N  45  
SY5  O01  H011  SING  N  N  46  
SY5  O04  H12   SING  N  N  47  
#   #
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
SY5  InChI             InChI                 1.03   "InChI=1S/C12H27N5O4/c1-17(8-12(20)21)16-11(19)6-9(14)5-10(18)7-15-4-2-3-13/h9-10,15,18H,2-8,13-14H2,1H3,(H,16,19)(H,20,21)/t9-,10-/m1/s1"  
SY5  InChIKey          InChI                 1.03   VBFFWDLIKBQABV-NXEZZACHSA-N  
SY5  SMILES_CANONICAL  CACTVS                3.385  "CN(CC(O)=O)NC(=O)C[C@H](N)C[C@@H](O)CNCCCN"  
SY5  SMILES            CACTVS                3.385  "CN(CC(O)=O)NC(=O)C[CH](N)C[CH](O)CNCCCN"  
SY5  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN(CC(=O)O)NC(=O)C[C@@H](C[C@H](CNCCCN)O)N"  
SY5  SMILES            "OpenEye OEToolkits"  2.0.7  "CN(CC(=O)O)NC(=O)CC(CC(CNCCCN)O)N"  
#
_pdbx_chem_comp_identifier.comp_id          SY5
_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       "2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     SY5
_pdbx_chem_comp_synonyms.name        "N6-(3-aminopropyl)-negamycin"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SY5  "Create component"  2020-12-03  PDBE  
SY5  "Initial release"   2021-05-26  RCSB  
##
