data_1JB
#

_chem_comp.id                                   1JB
_chem_comp.name                                 
;[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]
[(2R,3R,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
;

_chem_comp.type                                 SACCHARIDE
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H26 N2 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        dTDP-fucose
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-02-14
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       548.330
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    1JB
_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       4J7G
_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
1JB  N1   N1   N  0  1  N  N  N  -29.832  15.066  -13.979  -5.345   0.882   0.560  N1   1JB   1  
1JB  N3   N3   N  0  1  N  N  N  -29.936  14.771  -11.704  -6.183   1.608  -1.503  N3   1JB   2  
1JB  C4   C4   C  0  1  N  N  N  -30.453  13.532  -11.847  -6.638   2.744  -0.937  C4   1JB   3  
1JB  C5   C5   C  0  1  N  N  N  -30.687  13.021  -13.120  -6.436   2.961   0.447  C5   1JB   4  
1JB  C6   C6   C  0  1  N  N  N  -30.323  13.831  -14.184  -5.790   2.021   1.172  C6   1JB   5  
1JB  O1B  O1B  O  0  1  N  N  N  -33.103  13.964  -20.823   3.602  -1.660  -1.779  O1B  1JB   6  
1JB  PB   PB   P  0  1  N  N  N  -33.899  13.109  -19.889   3.307  -1.532  -0.334  PB   1JB   7  
1JB  O2B  O2B  O  0  1  N  N  N  -35.262  13.543  -19.505   3.831  -2.844   0.438  O2B  1JB   8  
1JB  O3B  O3B  O  0  1  N  N  N  -33.900  11.634  -20.597   4.050  -0.230   0.253  O3B  1JB   9  
1JB  C1Q  C1Q  C  0  1  N  N  R  -34.793  10.636  -20.112   5.457  -0.013   0.123  C1Q  1JB  10  
1JB  O5Q  O5Q  O  0  1  N  N  N  -35.906  10.758  -21.008   5.719   0.704  -1.086  O5Q  1JB  11  
1JB  C5Q  C5Q  C  0  1  N  N  R  -35.766  10.453  -22.387   5.066   1.973  -1.164  C5Q  1JB  12  
1JB  C6Q  C6Q  C  0  1  N  N  N  -36.988  10.886  -23.199   5.394   2.633  -2.505  C6Q  1JB  13  
1JB  C4Q  C4Q  C  0  1  N  N  R  -35.009   9.197  -22.782   5.553   2.868  -0.022  C4Q  1JB  14  
1JB  O4Q  O4Q  O  0  1  N  N  N  -36.008   8.267  -22.402   6.957   3.095  -0.159  O4Q  1JB  15  
1JB  C3Q  C3Q  C  0  1  N  N  S  -33.847   9.103  -21.800   5.275   2.172   1.315  C3Q  1JB  16  
1JB  O3Q  O3Q  O  0  1  N  N  N  -33.128   7.926  -22.179   5.793   2.967   2.384  O3Q  1JB  17  
1JB  C2Q  C2Q  C  0  1  N  N  R  -34.169   9.253  -20.331   5.960   0.802   1.317  C2Q  1JB  18  
1JB  O2Q  O2Q  O  0  1  N  N  N  -32.907   9.134  -19.642   5.647   0.114   2.530  O2Q  1JB  19  
1JB  O3A  O3A  O  0  1  N  N  N  -33.340  12.977  -18.369   1.718  -1.383  -0.123  O3A  1JB  20  
1JB  PA   PA   P  0  1  N  N  N  -31.865  12.525  -18.017   0.433  -2.142  -0.727  PA   1JB  21  
1JB  O1A  O1A  O  0  1  N  N  N  -31.795  11.383  -17.055   0.185  -1.655  -2.242  O1A  1JB  22  
1JB  O2A  O2A  O  0  1  N  N  N  -31.211  12.180  -19.338   0.670  -3.603  -0.712  O2A  1JB  23  
1JB  O5X  O5X  O  0  1  N  N  N  -31.168  13.909  -17.549  -0.862  -1.799   0.165  O5X  1JB  24  
1JB  C5X  C5X  C  0  1  N  N  N  -31.519  15.278  -17.762  -2.139  -2.403  -0.052  C5X  1JB  25  
1JB  C4X  C4X  C  0  1  N  N  R  -30.331  16.060  -17.206  -3.142  -1.856   0.966  C4X  1JB  26  
1JB  O4X  O4X  O  0  1  N  N  N  -30.610  16.251  -15.822  -3.386  -0.452   0.736  O4X  1JB  27  
1JB  C3X  C3X  C  0  1  N  N  S  -29.115  15.151  -17.247  -4.535  -2.504   0.763  C3X  1JB  28  
1JB  O3X  O3X  O  0  1  N  N  N  -28.182  15.688  -18.179  -4.633  -3.738   1.477  O3X  1JB  29  
1JB  C2X  C2X  C  0  1  N  N  N  -28.397  15.259  -15.912  -5.480  -1.438   1.370  C2X  1JB  30  
1JB  C1X  C1X  C  0  1  N  N  R  -29.444  15.962  -15.056  -4.650  -0.140   1.347  C1X  1JB  31  
1JB  C2   C2   C  0  1  N  N  N  -29.595  15.544  -12.748  -5.543   0.688  -0.757  C2   1JB  32  
1JB  O2   O2   O  0  1  N  N  N  -29.114  16.696  -12.623  -5.138  -0.332  -1.281  O2   1JB  33  
1JB  C5M  C5M  C  0  1  N  N  N  -31.277  11.648  -13.336  -6.935   4.222   1.104  C5M  1JB  34  
1JB  O4   O4   O  0  1  N  N  N  -30.753  12.850  -10.849  -7.218   3.577  -1.611  O4   1JB  35  
1JB  H1   H1   H  0  1  N  N  N  -29.801  15.129  -10.780  -6.318   1.452  -2.450  H1   1JB  36  
1JB  H2   H2   H  0  1  N  N  N  -30.435  13.465  -15.194  -5.627   2.169   2.229  H2   1JB  37  
1JB  H3   H3   H  0  1  N  N  N  -35.465  14.366  -19.933   3.670  -2.829   1.392  H3   1JB  38  
1JB  H4   H4   H  0  1  N  N  N  -35.074  10.785  -19.059   5.972  -0.973   0.095  H4   1JB  39  
1JB  H5   H5   H  0  1  N  N  N  -35.044  11.222  -22.699   3.988   1.833  -1.082  H5   1JB  40  
1JB  H6   H6   H  0  1  N  N  N  -37.405  11.809  -22.771   5.048   1.995  -3.318  H6   1JB  41  
1JB  H7   H7   H  0  1  N  N  N  -36.689  11.068  -24.242   4.896   3.601  -2.565  H7   1JB  42  
1JB  H8   H8   H  0  1  N  N  N  -37.749  10.092  -23.168   6.472   2.773  -2.587  H8   1JB  43  
1JB  H9   H9   H  0  1  N  N  N  -34.704   9.171  -23.839   5.025   3.820  -0.054  H9   1JB  44  
1JB  H10  H10  H  0  1  N  N  N  -35.705   7.385  -22.581   7.206   3.529  -0.986  H10  1JB  45  
1JB  H11  H11  H  0  1  N  N  N  -33.194   9.954  -22.043   4.200   2.043   1.442  H11  1JB  46  
1JB  H12  H12  H  0  1  N  N  N  -32.384   7.809  -21.600   5.652   2.586   3.261  H12  1JB  47  
1JB  H13  H13  H  0  1  N  N  N  -34.872   8.469  -20.013   7.039   0.934   1.240  H13  1JB  48  
1JB  H14  H14  H  0  1  N  N  N  -33.047   9.221  -18.706   6.049  -0.763   2.600  H14  1JB  49  
1JB  H15  H15  H  0  1  N  N  N  -31.348  10.651  -17.464   0.023  -0.706  -2.328  H15  1JB  50  
1JB  H16  H16  H  0  1  N  N  N  -31.654  15.484  -18.834  -2.484  -2.172  -1.060  H16  1JB  51  
1JB  H17  H17  H  0  1  N  N  N  -32.442  15.533  -17.220  -2.055  -3.483   0.065  H17  1JB  52  
1JB  H18  H18  H  0  1  N  N  N  -30.164  16.998  -17.755  -2.784  -2.022   1.983  H18  1JB  53  
1JB  H19  H19  H  0  1  N  N  N  -29.396  14.111  -17.470  -4.744  -2.651  -0.297  H19  1JB  54  
1JB  H20  H20  H  0  1  N  N  N  -27.414  15.130  -18.216  -5.487  -4.181   1.380  H20  1JB  55  
1JB  H21  H21  H  0  1  N  N  N  -28.149  14.266  -15.508  -6.375  -1.329   0.757  H21  1JB  56  
1JB  H22  H22  H  0  1  N  N  N  -27.479  15.860  -15.997  -5.746  -1.703   2.393  H22  1JB  57  
1JB  H23  H23  H  0  1  N  N  N  -29.013  16.886  -14.644  -4.492   0.217   2.364  H23  1JB  58  
1JB  H24  H24  H  0  1  N  N  N  -31.491  11.183  -12.362  -7.426   4.849   0.360  H24  1JB  59  
1JB  H25  H25  H  0  1  N  N  N  -32.210  11.736  -13.913  -7.646   3.966   1.890  H25  1JB  60  
1JB  H26  H26  H  0  1  N  N  N  -30.561  11.024  -13.891  -6.094   4.763   1.538  H26  1JB  61  
#   #
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
1JB  C6Q  C5Q  SING  N  N   1  
1JB  C4Q  O4Q  SING  N  N   2  
1JB  C4Q  C5Q  SING  N  N   3  
1JB  C4Q  C3Q  SING  N  N   4  
1JB  C5Q  O5Q  SING  N  N   5  
1JB  O3Q  C3Q  SING  N  N   6  
1JB  C3Q  C2Q  SING  N  N   7  
1JB  O5Q  C1Q  SING  N  N   8  
1JB  O1B  PB   DOUB  N  N   9  
1JB  O3B  C1Q  SING  N  N  10  
1JB  O3B  PB   SING  N  N  11  
1JB  C2Q  C1Q  SING  N  N  12  
1JB  C2Q  O2Q  SING  N  N  13  
1JB  PB   O2B  SING  N  N  14  
1JB  PB   O3A  SING  N  N  15  
1JB  O2A  PA   DOUB  N  N  16  
1JB  O3A  PA   SING  N  N  17  
1JB  O3X  C3X  SING  N  N  18  
1JB  PA   O5X  SING  N  N  19  
1JB  PA   O1A  SING  N  N  20  
1JB  C5X  O5X  SING  N  N  21  
1JB  C5X  C4X  SING  N  N  22  
1JB  C3X  C4X  SING  N  N  23  
1JB  C3X  C2X  SING  N  N  24  
1JB  C4X  O4X  SING  N  N  25  
1JB  C2X  C1X  SING  N  N  26  
1JB  O4X  C1X  SING  N  N  27  
1JB  C1X  N1   SING  N  N  28  
1JB  C6   N1   SING  N  N  29  
1JB  C6   C5   DOUB  N  N  30  
1JB  N1   C2   SING  N  N  31  
1JB  C5M  C5   SING  N  N  32  
1JB  C5   C4   SING  N  N  33  
1JB  C2   O2   DOUB  N  N  34  
1JB  C2   N3   SING  N  N  35  
1JB  C4   N3   SING  N  N  36  
1JB  C4   O4   DOUB  N  N  37  
1JB  N3   H1   SING  N  N  38  
1JB  C6   H2   SING  N  N  39  
1JB  O2B  H3   SING  N  N  40  
1JB  C1Q  H4   SING  N  N  41  
1JB  C5Q  H5   SING  N  N  42  
1JB  C6Q  H6   SING  N  N  43  
1JB  C6Q  H7   SING  N  N  44  
1JB  C6Q  H8   SING  N  N  45  
1JB  C4Q  H9   SING  N  N  46  
1JB  O4Q  H10  SING  N  N  47  
1JB  C3Q  H11  SING  N  N  48  
1JB  O3Q  H12  SING  N  N  49  
1JB  C2Q  H13  SING  N  N  50  
1JB  O2Q  H14  SING  N  N  51  
1JB  O1A  H15  SING  N  N  52  
1JB  C5X  H16  SING  N  N  53  
1JB  C5X  H17  SING  N  N  54  
1JB  C4X  H18  SING  N  N  55  
1JB  C3X  H19  SING  N  N  56  
1JB  O3X  H20  SING  N  N  57  
1JB  C2X  H21  SING  N  N  58  
1JB  C2X  H22  SING  N  N  59  
1JB  C1X  H23  SING  N  N  60  
1JB  C5M  H24  SING  N  N  61  
1JB  C5M  H25  SING  N  N  62  
1JB  C5M  H26  SING  N  N  63  
#   #
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
1JB  SMILES            ACDLabs               12.01  "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)C)O)O)C"  
1JB  InChI             InChI                 1.03   "InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8+,9-,10-,11+,12+,13-,15-/m1/s1"  
1JB  InChIKey          InChI                 1.03   ZOSQFDVXNQFKBY-FQLHZTMTSA-N  
1JB  SMILES_CANONICAL  CACTVS                3.370  "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O"  
1JB  SMILES            CACTVS                3.370  "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O"  
1JB  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O"  
1JB  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)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
1JB  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
1JB  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] 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
1JB  "Create component"  2013-02-14  RCSB  
1JB  "Initial release"   2013-05-22  RCSB  
1JB  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     1JB
_pdbx_chem_comp_synonyms.name        dTDP-fucose
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
