data_B31
#

_chem_comp.id                                   B31
_chem_comp.name                                 "(2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H41 N5 O12"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Butirosin A"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-05-10
_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                       555.577
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    B31
_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       3H8P
_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
B31  C01   C01   C  0  1  N  N  R  52.210  29.318  15.101  -2.608   0.160  -0.419  C01   B31   1  
B31  C02   C02   C  0  1  N  N  N  51.912  29.849  16.508  -2.299  -1.322  -0.196  C02   B31   2  
B31  C03   C03   C  0  1  N  N  S  52.210  31.361  16.509  -0.832  -1.594  -0.537  C03   B31   3  
B31  C04   C04   C  0  1  N  N  R  51.295  32.107  15.501   0.067  -0.745   0.363  C04   B31   4  
B31  C05   C05   C  0  1  N  N  R  51.559  31.536  14.070  -0.243   0.737   0.140  C05   B31   5  
B31  C06   C06   C  0  1  N  N  S  51.305  30.008  14.065  -1.709   1.009   0.481  C06   B31   6  
B31  N01   N01   N  0  1  N  N  N  51.851  27.907  15.090  -4.012   0.420  -0.092  N01   B31   7  
B31  N03   N03   N  0  1  N  N  N  51.874  31.859  17.871  -0.536  -3.017  -0.324  N03   B31   8  
B31  O04   O04   O  0  1  N  N  N  51.662  33.484  15.591   1.436  -0.999   0.044  O04   B31   9  
B31  O05   O05   O  0  1  N  N  N  50.658  32.142  13.154   0.597   1.531   0.981  O05   B31  10  
B31  O06   O06   O  0  1  N  N  N  51.636  29.479  12.782  -1.998   2.393   0.273  O06   B31  11  
B31  C11   C11   C  0  1  N  N  R  50.650  34.333  15.044   2.213  -1.466   1.149  C11   B31  12  
B31  C12   C12   C  0  1  N  N  R  51.293  35.639  14.558   3.681  -1.086   0.938  C12   B31  13  
B31  C13   C13   C  0  1  N  N  R  51.785  36.483  15.728   4.203  -1.779  -0.324  C13   B31  14  
B31  C14   C14   C  0  1  N  N  S  50.643  36.707  16.682   4.010  -3.292  -0.180  C14   B31  15  
B31  C15   C15   C  0  1  N  N  R  50.197  35.355  17.226   2.529  -3.587   0.074  C15   B31  16  
B31  C16   C16   C  0  1  N  N  N  49.032  35.575  18.190   2.336  -5.090   0.279  C16   B31  17  
B31  N12   N12   N  0  1  N  N  N  52.506  35.253  13.781   3.793   0.370   0.781  N12   B31  18  
B31  N16   N16   N  0  1  N  N  N  48.806  34.243  18.841   0.919  -5.371   0.543  N16   B31  19  
B31  O11   O11   O  0  1  N  N  N  49.713  34.521  16.144   2.099  -2.887   1.244  O11   B31  20  
B31  O13   O13   O  0  1  N  N  N  52.211  37.734  15.219   5.593  -1.489  -0.488  O13   B31  21  
B31  O14   O14   O  0  1  N  N  N  51.104  37.516  17.755   4.427  -3.943  -1.381  O14   B31  22  
B31  C21   C21   C  0  1  N  N  S  51.324  32.317  11.893   0.912   2.816   0.442  C21   B31  23  
B31  C22   C22   C  0  1  N  N  R  50.390  31.820  10.828   1.719   3.632   1.470  C22   B31  24  
B31  C23   C23   C  0  1  N  N  R  49.692  33.044  10.353   3.042   3.963   0.738  C23   B31  25  
B31  C24   C24   C  0  1  N  N  R  50.649  34.169  10.703   2.642   3.791  -0.750  C24   B31  26  
B31  C25   C25   C  0  1  N  N  N  49.918  35.445  11.079   3.871   3.475  -1.605  C25   B31  27  
B31  O21   O21   O  0  1  N  N  N  51.443  33.725  11.807   1.733   2.667  -0.729  O21   B31  28  
B31  O22   O22   O  0  1  N  N  N  51.168  31.286   9.761   1.022   4.831   1.815  O22   B31  29  
B31  O23   O23   O  0  1  N  N  N  48.487  33.171  11.112   4.070   3.038   1.100  O23   B31  30  
B31  O25   O25   O  0  1  N  N  N  50.883  36.487  11.147   3.494   3.436  -2.983  O25   B31  31  
B31  C51   C51   C  0  1  N  N  N  52.737  26.990  14.529  -4.969   0.214  -1.019  C51   B31  32  
B31  C52   C52   C  0  1  N  N  S  52.262  25.541  14.558  -6.414   0.482  -0.683  C52   B31  33  
B31  C53   C53   C  0  1  N  N  N  52.248  24.921  13.158  -6.873  -0.491   0.405  C53   B31  34  
B31  C54   C54   C  0  1  N  N  N  51.267  25.628  12.217  -8.299  -0.140   0.835  C54   B31  35  
B31  N54   N54   N  0  1  N  N  N  51.481  25.149  10.840  -8.740  -1.074   1.879  N54   B31  36  
B31  O51   O51   O  0  1  N  N  N  53.808  27.309  14.044  -4.668  -0.187  -2.123  O51   B31  37  
B31  O52   O52   O  0  1  N  N  N  50.938  25.459  15.095  -7.216   0.303  -1.852  O52   B31  38  
B31  H01   H01   H  0  1  N  N  N  53.268  29.497  14.857  -2.424   0.416  -1.462  H01   B31  39  
B31  H02   H02   H  0  1  N  N  N  50.857  29.672  16.763  -2.483  -1.579   0.847  H02   B31  40  
B31  H02A  H02A  H  0  0  N  N  N  52.534  29.333  17.254  -2.940  -1.927  -0.838  H02A  B31  41  
B31  H03   H03   H  0  1  N  N  N  53.261  31.534  16.233  -0.649  -1.337  -1.581  H03   B31  42  
B31  H04   H04   H  0  1  N  N  N  50.223  31.982  15.715  -0.117  -1.001   1.406  H04   B31  43  
B31  H05   H05   H  0  1  N  N  N  52.600  31.745  13.782  -0.059   0.994  -0.903  H05   B31  44  
B31  H06   H06   H  0  1  N  N  N  50.247  29.828  14.305  -1.893   0.752   1.525  H06   B31  45  
B31  HN01  HN01  H  0  0  N  N  N  50.982  27.601  15.479  -4.253   0.741   0.791  HN01  B31  46  
B31  HN03  HN03  H  0  0  N  N  N  51.799  31.085  18.500  -1.019  -3.592  -0.997  HN03  B31  47  
B31  HN0A  HN0A  H  0  0  N  N  N  52.594  32.477  18.187   0.458  -3.187  -0.350  HN0A  B31  48  
B31  HO06  HO06  H  0  0  N  N  N  51.710  30.189  12.155  -2.912   2.638   0.471  HO06  B31  49  
B31  H11   H11   H  0  1  N  N  N  50.132  33.920  14.166   1.848  -1.010   2.069  H11   B31  50  
B31  H12   H12   H  0  1  N  N  N  50.554  36.212  13.978   4.267  -1.406   1.799  H12   B31  51  
B31  H13   H13   H  0  1  N  N  N  52.611  35.977  16.249   3.650  -1.421  -1.192  H13   B31  52  
B31  H14   H14   H  0  1  N  N  N  49.803  37.203  16.174   4.603  -3.657   0.659  H14   B31  53  
B31  H15   H15   H  0  1  N  N  N  51.049  34.872  17.727   1.941  -3.258  -0.783  H15   B31  54  
B31  H16   H16   H  0  1  N  N  N  49.281  36.342  18.939   2.651  -5.623  -0.619  H16   B31  55  
B31  H16A  H16A  H  0  0  N  N  N  48.132  35.935  17.670   2.936  -5.422   1.126  H16A  B31  56  
B31  HN12  HN12  H  0  0  N  N  N  52.269  35.167  12.813   3.450   0.850   1.599  HN12  B31  57  
B31  HN1A  HN1A  H  0  0  N  N  N  53.209  35.955  13.890   4.744   0.640   0.576  HN1A  B31  58  
B31  HN16  HN16  H  0  0  N  N  N  48.756  33.533  18.139   0.760  -6.361   0.651  HN16  B31  59  
B31  HN1B  HN1B  H  0  0  N  N  N  49.563  34.044  19.463   0.594  -4.862   1.352  HN1B  B31  60  
B31  HO13  HO13  H  0  0  N  N  N  52.306  38.352  15.935   5.990  -1.897  -1.270  HO13  B31  61  
B31  HO14  HO14  H  0  0  N  N  N  51.207  36.982  18.534   5.356  -3.795  -1.607  HO14  B31  62  
B31  H21   H21   H  0  1  N  N  N  52.287  31.796  11.790  -0.006   3.345   0.186  H21   B31  63  
B31  H22   H22   H  0  1  N  N  N  49.695  31.045  11.185   1.915   3.036   2.362  H22   B31  64  
B31  H23   H23   H  0  1  N  N  N  49.437  33.037   9.283   3.354   4.988   0.941  H23   B31  65  
B31  H24   H24   H  0  1  N  N  N  51.269  34.404   9.825   2.139   4.685  -1.118  H24   B31  66  
B31  H25   H25   H  0  1  N  N  N  49.157  35.683  10.321   4.625   4.247  -1.456  H25   B31  67  
B31  H25A  H25A  H  0  0  N  N  N  49.408  35.327  12.047   4.278   2.507  -1.312  H25A  B31  68  
B31  HO22  HO22  H  0  0  N  N  N  50.618  31.167   8.996   0.159   4.680   2.225  HO22  B31  69  
B31  HO23  HO23  H  0  0  N  N  N  48.697  33.199  12.038   4.292   3.046   2.041  HO23  B31  70  
B31  HO25  HO25  H  0  0  N  N  N  51.098  36.661  12.056   4.225   3.241  -3.585  HO25  B31  71  
B31  H52   H52   H  0  1  N  N  N  52.970  24.987  15.192  -6.519   1.505  -0.323  H52   B31  72  
B31  H53   H53   H  0  1  N  N  N  53.259  24.999  12.731  -6.852  -1.509   0.015  H53   B31  73  
B31  H53A  H53A  H  0  0  N  N  N  51.926  23.874  13.256  -6.206  -0.417   1.264  H53A  B31  74  
B31  H54   H54   H  0  1  N  N  N  50.235  25.406  12.527  -8.320   0.878   1.225  H54   B31  75  
B31  H54A  H54A  H  0  0  N  N  N  51.435  26.714  12.259  -8.966  -0.213  -0.024  H54A  B31  76  
B31  HN54  HN54  H  0  0  N  N  N  51.529  25.931  10.218  -9.679  -0.862   2.180  HN54  B31  77  
B31  HN5A  HN5A  H  0  0  N  N  N  52.337  24.634  10.796  -8.668  -2.029   1.563  HN5A  B31  78  
B31  HO52  HO52  H  0  0  N  N  N  50.981  25.441  16.044  -7.170  -0.587  -2.227  HO52  B31  79  
#   #
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
B31  C06  C01   SING  N  N   1  
B31  N01  C01   SING  N  N   2  
B31  C01  C02   SING  N  N   3  
B31  C01  H01   SING  N  N   4  
B31  C02  C03   SING  N  N   5  
B31  C02  H02   SING  N  N   6  
B31  C02  H02A  SING  N  N   7  
B31  C04  C03   SING  N  N   8  
B31  C03  N03   SING  N  N   9  
B31  C03  H03   SING  N  N  10  
B31  C05  C04   SING  N  N  11  
B31  C04  O04   SING  N  N  12  
B31  C04  H04   SING  N  N  13  
B31  O05  C05   SING  N  N  14  
B31  C06  C05   SING  N  N  15  
B31  C05  H05   SING  N  N  16  
B31  O06  C06   SING  N  N  17  
B31  C06  H06   SING  N  N  18  
B31  C51  N01   SING  N  N  19  
B31  N01  HN01  SING  N  N  20  
B31  N03  HN03  SING  N  N  21  
B31  N03  HN0A  SING  N  N  22  
B31  C11  O04   SING  N  N  23  
B31  C21  O05   SING  N  N  24  
B31  O06  HO06  SING  N  N  25  
B31  C12  C11   SING  N  N  26  
B31  C11  O11   SING  N  N  27  
B31  C11  H11   SING  N  N  28  
B31  N12  C12   SING  N  N  29  
B31  C12  C13   SING  N  N  30  
B31  C12  H12   SING  N  N  31  
B31  O13  C13   SING  N  N  32  
B31  C13  C14   SING  N  N  33  
B31  C13  H13   SING  N  N  34  
B31  C14  C15   SING  N  N  35  
B31  C14  O14   SING  N  N  36  
B31  C14  H14   SING  N  N  37  
B31  O11  C15   SING  N  N  38  
B31  C15  C16   SING  N  N  39  
B31  C15  H15   SING  N  N  40  
B31  C16  N16   SING  N  N  41  
B31  C16  H16   SING  N  N  42  
B31  C16  H16A  SING  N  N  43  
B31  N12  HN12  SING  N  N  44  
B31  N12  HN1A  SING  N  N  45  
B31  N16  HN16  SING  N  N  46  
B31  N16  HN1B  SING  N  N  47  
B31  O13  HO13  SING  N  N  48  
B31  O14  HO14  SING  N  N  49  
B31  C22  C21   SING  N  N  50  
B31  O21  C21   SING  N  N  51  
B31  C21  H21   SING  N  N  52  
B31  O22  C22   SING  N  N  53  
B31  C23  C22   SING  N  N  54  
B31  C22  H22   SING  N  N  55  
B31  C23  C24   SING  N  N  56  
B31  C23  O23   SING  N  N  57  
B31  C23  H23   SING  N  N  58  
B31  C24  C25   SING  N  N  59  
B31  C24  O21   SING  N  N  60  
B31  C24  H24   SING  N  N  61  
B31  C25  O25   SING  N  N  62  
B31  C25  H25   SING  N  N  63  
B31  C25  H25A  SING  N  N  64  
B31  O22  HO22  SING  N  N  65  
B31  O23  HO23  SING  N  N  66  
B31  O25  HO25  SING  N  N  67  
B31  O51  C51   DOUB  N  N  68  
B31  C51  C52   SING  N  N  69  
B31  C53  C52   SING  N  N  70  
B31  C52  O52   SING  N  N  71  
B31  C52  H52   SING  N  N  72  
B31  C54  C53   SING  N  N  73  
B31  C53  H53   SING  N  N  74  
B31  C53  H53A  SING  N  N  75  
B31  N54  C54   SING  N  N  76  
B31  C54  H54   SING  N  N  77  
B31  C54  H54A  SING  N  N  78  
B31  N54  HN54  SING  N  N  79  
B31  N54  HN5A  SING  N  N  80  
B31  O52  HO52  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
B31  SMILES            ACDLabs               10.04  "O=C(NC3C(O)C(OC1OC(C(O)C1O)CO)C(OC2OC(CN)C(O)C(O)C2N)C(N)C3)C(O)CCN"  
B31  SMILES_CANONICAL  CACTVS                3.341  "NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2N)[C@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H]3O)[C@H]1O"  
B31  SMILES            CACTVS                3.341  "NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)[CH](O)[CH](O)[CH]2N)[CH](O[CH]3O[CH](CO)[CH](O)[CH]3O)[CH]1O"  
B31  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)O)O[C@H]2[C@@H]([C@H]([C@H](O2)CO)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N"  
B31  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(C(C(C1NC(=O)C(CCN)O)O)OC2C(C(C(O2)CO)O)O)OC3C(C(C(C(O3)CN)O)O)N)N"  
B31  InChI             InChI                 1.03   "InChI=1S/C21H41N5O12/c22-2-1-8(28)19(34)26-7-3-6(24)17(37-20-11(25)15(32)13(30)9(4-23)35-20)18(12(7)29)38-21-16(33)14(31)10(5-27)36-21/h6-18,20-21,27-33H,1-5,22-25H2,(H,26,34)/t6-,7+,8-,9+,10+,11+,12-,13+,14-,15+,16+,17+,18+,20+,21-/m0/s1"  
B31  InChIKey          InChI                 1.03   XEQLFNPSYWZPOW-SVRMBHBBSA-N  
#   #
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
B31  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide"  
B31  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxy-oxan-2-yl]oxy-3-[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-2-hydroxy-cyclohexyl]-2-hydroxy-butanamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
B31  "Create component"   2009-05-10  RCSB  
B31  "Modify descriptor"  2011-06-04  RCSB  
B31  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     B31
_pdbx_chem_comp_synonyms.name        "Butirosin A"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
