data_GBO
#

_chem_comp.id                                   GBO
_chem_comp.name                                 "(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H35 N3 O9 P2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        Biotin-GPP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2008-10-15
_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                       555.519
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GBO
_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       3EU5
_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
GBO  O2    O2    O  0  1  N  N  N  54.796  -43.036   7.611    9.667  -3.273  -1.360  O2    GBO   1  
GBO  P1    P1    P  0  1  N  N  N  54.157  -42.406   6.279    9.442  -2.926   0.195  P1    GBO   2  
GBO  O8    O8    O  0  1  N  N  N  53.285  -41.235   6.897    9.006  -4.259   0.985  O8    GBO   3  
GBO  O1    O1    O  0  1  N  N  N  55.173  -42.042   5.272   10.701  -2.401   0.770  O1    GBO   4  
GBO  O3    O3    O  0  1  N  N  N  53.112  -43.485   5.749    8.284  -1.816   0.336  O3    GBO   5  
GBO  P2    P2    P  0  1  N  N  R  52.720  -43.748   4.195    8.217  -0.230   0.065  P2    GBO   6  
GBO  O4    O4    O  0  1  N  N  N  51.790  -44.876   4.277    8.982   0.549   1.248  O4    GBO   7  
GBO  O9    O9    O  0  1  N  N  N  52.323  -42.537   3.401    8.865   0.078  -1.229  O9    GBO   8  
GBO  O5    O5    O  0  1  N  N  N  54.148  -44.310   3.811    6.678   0.241   0.019  O5    GBO   9  
GBO  C1    C1    C  0  1  N  N  N  54.705  -44.390   2.531    6.281   1.575  -0.307  C1    GBO  10  
GBO  C2    C2    C  0  1  N  N  N  56.002  -44.864   2.654    4.779   1.678  -0.259  C2    GBO  11  
GBO  C3    C3    C  0  1  N  N  N  56.735  -45.211   1.548    4.134   2.298  -1.216  C3    GBO  12  
GBO  C4    C4    C  0  1  N  N  N  56.092  -45.046   0.144    4.899   3.016  -2.298  C4    GBO  13  
GBO  C5    C5    C  0  1  N  N  N  58.163  -45.742   1.610    2.627   2.294  -1.235  C5    GBO  14  
GBO  C6    C6    C  0  1  N  N  N  58.505  -46.600   2.819    2.105   3.563  -0.559  C6    GBO  15  
GBO  C7    C7    C  0  1  N  N  N  59.624  -47.362   2.502    0.598   3.559  -0.578  C7    GBO  16  
GBO  C8    C8    C  0  1  N  N  N  60.223  -48.336   3.269   -0.071   3.608   0.547  C8    GBO  17  
GBO  C9    C9    C  0  1  N  N  N  59.595  -48.674   4.619    0.660   3.535   1.863  C9    GBO  18  
GBO  C10   C10   C  0  1  N  N  N  61.444  -49.126   2.757   -1.573   3.736   0.525  C10   GBO  19  
GBO  N1    N1    N  0  1  N  N  N  60.817  -50.398   2.467   -2.178   2.406   0.628  N1    GBO  20  
GBO  C11   C11   C  0  1  N  N  N  61.350  -51.575   2.192   -3.519   2.274   0.629  C11   GBO  21  
GBO  O6    O6    O  0  1  N  N  N  62.547  -51.844   2.093   -4.225   3.257   0.544  O6    GBO  22  
GBO  C12   C12   C  0  1  N  N  N  60.271  -52.676   1.932   -4.142   0.906   0.734  C12   GBO  23  
GBO  C13   C13   C  0  1  N  N  N  59.196  -52.897   3.051   -5.667   1.037   0.712  C13   GBO  24  
GBO  C14   C14   C  0  1  N  N  N  58.066  -53.791   2.523   -6.299  -0.352   0.820  C14   GBO  25  
GBO  C15   C15   C  0  1  N  N  N  56.677  -53.264   2.898   -7.823  -0.222   0.798  C15   GBO  26  
GBO  C16   C16   C  0  1  N  N  S  55.578  -54.266   2.423   -8.455  -1.611   0.905  C16   GBO  27  
GBO  S1    S1    S  0  1  N  N  N  56.140  -55.706   1.387   -8.151  -2.586  -0.624  S1    GBO  28  
GBO  C17   C17   C  0  1  N  N  N  54.428  -56.118   0.878   -9.654  -3.629  -0.444  C17   GBO  29  
GBO  C18   C18   C  0  1  N  N  R  53.772  -54.723   0.654  -10.672  -2.653   0.178  C18   GBO  30  
GBO  C19   C19   C  0  1  N  N  S  54.489  -53.606   1.500   -9.993  -1.510   0.947  C19   GBO  31  
GBO  N2    N2    N  0  1  N  N  N  55.148  -52.759   0.465  -10.414  -0.297   0.228  N2    GBO  32  
GBO  C20   C20   C  0  1  N  N  N  54.917  -53.245  -0.749  -11.207  -0.648  -0.794  C20   GBO  33  
GBO  O7    O7    O  0  1  N  N  N  55.364  -52.749  -1.785  -11.699   0.159  -1.558  O7    GBO  34  
GBO  N3    N3    N  0  1  N  N  N  54.132  -54.329  -0.714  -11.411  -1.973  -0.897  N3    GBO  35  
GBO  HO2   HO2   H  0  1  N  N  N  55.730  -43.160   7.487    8.881  -3.623  -1.803  HO2   GBO  36  
GBO  HO8   HO8   H  0  1  N  N  N  53.111  -41.419   7.813    9.658  -4.972   0.944  HO8   GBO  37  
GBO  HO4   HO4   H  0  1  N  N  N  51.589  -45.185   3.402    8.609   0.394   2.126  HO4   GBO  38  
GBO  H1    H1    H  0  1  N  N  N  54.113  -45.075   1.907    6.717   2.269   0.412  H1    GBO  39  
GBO  H1A   H1A   H  0  1  N  N  N  54.706  -43.399   2.054    6.631   1.823  -1.309  H1A   GBO  40  
GBO  H2    H2    H  0  1  N  N  N  56.442  -44.961   3.636    4.233   1.241   0.565  H2    GBO  41  
GBO  H4    H4    H  0  1  N  N  N  54.997  -45.007   0.244    5.173   2.308  -3.080  H4    GBO  42  
GBO  H4A   H4A   H  0  1  N  N  N  56.451  -44.114  -0.316    4.277   3.803  -2.722  H4A   GBO  43  
GBO  H4B   H4B   H  0  1  N  N  N  56.372  -45.900  -0.490    5.802   3.456  -1.874  H4B   GBO  44  
GBO  H5    H5    H  0  1  N  N  N  58.322  -46.360   0.714    2.277   2.261  -2.267  H5    GBO  45  
GBO  H5A   H5A   H  0  1  N  N  N  58.810  -44.855   1.679    2.260   1.419  -0.699  H5A   GBO  46  
GBO  H6    H6    H  0  1  N  N  N  58.721  -45.958   3.686    2.455   3.596   0.473  H6    GBO  47  
GBO  H6A   H6A   H  0  1  N  N  N  57.658  -47.254   3.075    2.473   4.438  -1.095  H6A   GBO  48  
GBO  H7    H7    H  0  1  N  N  N  60.077  -47.167   1.541    0.070   3.516  -1.519  H7    GBO  49  
GBO  H9    H9    H  0  1  N  N  N  60.384  -48.755   5.381    0.979   4.535   2.157  H9    GBO  50  
GBO  H9A   H9A   H  0  1  N  N  N  58.890  -47.879   4.905   -0.004   3.126   2.625  H9A   GBO  51  
GBO  H9B   H9B   H  0  1  N  N  N  59.058  -49.631   4.544    1.533   2.891   1.758  H9B   GBO  52  
GBO  H10   H10   H  0  1  N  N  N  61.906  -48.667   1.870   -1.897   4.349   1.367  H10   GBO  53  
GBO  H10A  H10A  H  0  0  N  N  N  62.286  -49.179   3.463   -1.884   4.206  -0.408  H10A  GBO  54  
GBO  HN1   HN1   H  0  1  N  N  N  59.817  -50.383   2.476   -1.614   1.620   0.696  HN1   GBO  55  
GBO  H12   H12   H  0  1  N  N  N  59.731  -52.388   1.018   -3.818   0.293  -0.107  H12   GBO  56  
GBO  H12A  H12A  H  0  0  N  N  N  60.829  -53.622   1.875   -3.831   0.436   1.667  H12A  GBO  57  
GBO  H13   H13   H  0  1  N  N  N  59.668  -53.382   3.918   -5.991   1.649   1.554  H13   GBO  58  
GBO  H13A  H13A  H  0  0  N  N  N  58.778  -51.924   3.348   -5.978   1.506  -0.221  H13A  GBO  59  
GBO  H14   H14   H  0  1  N  N  N  58.138  -53.833   1.426   -5.975  -0.965  -0.021  H14   GBO  60  
GBO  H14A  H14A  H  0  0  N  N  N  58.183  -54.785   2.980   -5.988  -0.822   1.753  H14A  GBO  61  
GBO  H15   H15   H  0  1  N  N  N  56.615  -53.148   3.990   -8.148   0.391   1.639  H15   GBO  62  
GBO  H15A  H15A  H  0  0  N  N  N  56.515  -52.292   2.408   -8.134   0.248  -0.135  H15A  GBO  63  
GBO  H16   H16   H  0  1  N  N  N  55.212  -54.602   3.404   -8.079  -2.139   1.781  H16   GBO  64  
GBO  H17   H17   H  0  1  N  N  N  54.414  -56.723  -0.041  -10.000  -3.980  -1.416  H17   GBO  65  
GBO  H17A  H17A  H  0  0  N  N  N  53.895  -56.725   1.625   -9.464  -4.470   0.223  H17A  GBO  66  
GBO  H18   H18   H  0  1  N  N  N  52.701  -54.802   0.893  -11.358  -3.190   0.833  H18   GBO  67  
GBO  H19   H19   H  0  1  N  N  N  53.805  -53.040   2.150  -10.347  -1.486   1.978  H19   GBO  68  
GBO  HN2   HN2   H  0  1  N  N  N  55.688  -51.940   0.658  -10.159   0.610   0.457  HN2   GBO  69  
GBO  HN3   HN3   H  0  1  N  N  N  53.824  -54.817  -1.531  -11.955  -2.408  -1.573  HN3   GBO  70  
#   #
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
GBO  P1   O2    SING  N  N   1  
GBO  O2   HO2   SING  N  N   2  
GBO  O1   P1    DOUB  N  N   3  
GBO  O3   P1    SING  N  N   4  
GBO  P1   O8    SING  N  N   5  
GBO  O8   HO8   SING  N  N   6  
GBO  P2   O3    SING  N  N   7  
GBO  O9   P2    DOUB  N  N   8  
GBO  O5   P2    SING  N  N   9  
GBO  P2   O4    SING  N  N  10  
GBO  O4   HO4   SING  N  N  11  
GBO  C1   O5    SING  N  N  12  
GBO  C1   C2    SING  N  N  13  
GBO  C1   H1    SING  N  N  14  
GBO  C1   H1A   SING  N  N  15  
GBO  C3   C2    DOUB  N  N  16  
GBO  C2   H2    SING  N  E  17  
GBO  C4   C3    SING  N  N  18  
GBO  C3   C5    SING  N  N  19  
GBO  C4   H4    SING  N  N  20  
GBO  C4   H4A   SING  N  N  21  
GBO  C4   H4B   SING  N  N  22  
GBO  C5   C6    SING  N  N  23  
GBO  C5   H5    SING  N  N  24  
GBO  C5   H5A   SING  N  N  25  
GBO  C7   C6    SING  N  N  26  
GBO  C6   H6    SING  N  N  27  
GBO  C6   H6A   SING  N  N  28  
GBO  C7   C8    DOUB  N  E  29  
GBO  C7   H7    SING  N  N  30  
GBO  C10  C8    SING  N  N  31  
GBO  C8   C9    SING  N  N  32  
GBO  C9   H9    SING  N  N  33  
GBO  C9   H9A   SING  N  N  34  
GBO  C9   H9B   SING  N  N  35  
GBO  N1   C10   SING  N  N  36  
GBO  C10  H10   SING  N  N  37  
GBO  C10  H10A  SING  N  N  38  
GBO  C11  N1    SING  N  N  39  
GBO  N1   HN1   SING  N  N  40  
GBO  C12  C11   SING  N  N  41  
GBO  O6   C11   DOUB  N  N  42  
GBO  C12  C13   SING  N  N  43  
GBO  C12  H12   SING  N  N  44  
GBO  C12  H12A  SING  N  N  45  
GBO  C14  C13   SING  N  N  46  
GBO  C13  H13   SING  N  N  47  
GBO  C13  H13A  SING  N  N  48  
GBO  C14  C15   SING  N  N  49  
GBO  C14  H14   SING  N  N  50  
GBO  C14  H14A  SING  N  N  51  
GBO  C16  C15   SING  N  N  52  
GBO  C15  H15   SING  N  N  53  
GBO  C15  H15A  SING  N  N  54  
GBO  S1   C16   SING  N  N  55  
GBO  C19  C16   SING  N  N  56  
GBO  C16  H16   SING  N  N  57  
GBO  C17  S1    SING  N  N  58  
GBO  C18  C17   SING  N  N  59  
GBO  C17  H17   SING  N  N  60  
GBO  C17  H17A  SING  N  N  61  
GBO  N3   C18   SING  N  N  62  
GBO  C18  C19   SING  N  N  63  
GBO  C18  H18   SING  N  N  64  
GBO  N2   C19   SING  N  N  65  
GBO  C19  H19   SING  N  N  66  
GBO  C20  N2    SING  N  N  67  
GBO  N2   HN2   SING  N  N  68  
GBO  O7   C20   DOUB  N  N  69  
GBO  C20  N3    SING  N  N  70  
GBO  N3   HN3   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
GBO  SMILES            ACDLabs               10.04  "O=C1NC2C(SCC2N1)CCCCC(=O)NCC(=C/CCC(=C/COP(=O)(O)OP(=O)(O)O)/C)/C"  
GBO  SMILES_CANONICAL  CACTVS                3.341  "C\C(CC\C=C(/C)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)=C/CO[P@](O)(=O)O[P](O)(O)=O"  
GBO  SMILES            CACTVS                3.341  "CC(CCC=C(C)CNC(=O)CCCC[CH]1SC[CH]2NC(=O)N[CH]12)=CCO[P](O)(=O)O[P](O)(O)=O"  
GBO  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)/CC\C=C(/C)\CNC(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2"  
GBO  SMILES            "OpenEye OEToolkits"  1.5.0  "CC(=CCOP(=O)(O)OP(=O)(O)O)CCC=C(C)CNC(=O)CCCCC1C2C(CS1)NC(=O)N2"  
GBO  InChI             InChI                 1.03   "InChI=1S/C20H35N3O9P2S/c1-14(10-11-31-34(29,30)32-33(26,27)28)6-5-7-15(2)12-21-18(24)9-4-3-8-17-19-16(13-35-17)22-20(25)23-19/h7,10,16-17,19H,3-6,8-9,11-13H2,1-2H3,(H,21,24)(H,29,30)(H2,22,23,25)(H2,26,27,28)/b14-10+,15-7+/t16-,17-,19-/m0/s1"  
GBO  InChIKey          InChI                 1.03   XZJFCDBLIMGOSX-VRLLXNLQSA-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
GBO  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate"  
GBO  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2E,6E)-8-[5-[(3aR,6S,6aS)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-6-yl]pentanoylamino]-3,7-dimethyl-octa-2,6-dienyl] phosphono hydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GBO  "Create component"   2008-10-15  PDBJ  
GBO  "Modify descriptor"  2011-06-04  RCSB  
GBO  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     GBO
_pdbx_chem_comp_synonyms.name        Biotin-GPP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
