data_12V
#

_chem_comp.id                                   12V
_chem_comp.name                                 "(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H27 N3 O16 P2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-06-19
_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                       623.419
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    12V
_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       ?
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
12V  N1      N1      N  0  1  N  N  N  114.009  48.435  61.842   6.095  -1.171   0.526  N1      12V   1  
12V  C2      C2      C  0  1  N  N  N  114.899  47.663  61.192   6.342  -1.101  -0.795  C2      12V   2  
12V  O2      O2      O  0  1  N  N  N  114.771  47.448  59.984   6.014  -0.108  -1.415  O2      12V   3  
12V  N3      N3      N  0  1  N  N  N  115.956  47.069  61.865   6.949  -2.115  -1.439  N3      12V   4  
12V  C4      C4      C  0  1  N  N  N  116.102  47.296  63.204   7.319  -3.224  -0.767  C4      12V   5  
12V  O4      O4      O  0  1  N  N  N  117.040  46.775  63.785   7.868  -4.141  -1.349  O4      12V   6  
12V  C5      C5      C  0  1  N  N  N  115.197  48.098  63.885   7.064  -3.310   0.623  C5      12V   7  
12V  C6      C6      C  0  1  N  N  N  114.142  48.690  63.208   6.454  -2.278   1.245  C6      12V   8  
12V  PA      PA      P  0  1  N  N  N  110.392  54.319  62.765   0.398   2.136  -0.839  PA      12V   9  
12V  PB      PB      P  0  1  N  N  N  107.895  53.632  63.926  -2.199   0.791  -1.325  PB      12V  10  
12V  "C1'"   "C1'"   C  0  1  N  N  S  106.933  55.319  62.242  -4.610  -0.157  -0.673  "C1'"   12V  11  
12V  "O1'"   "O1'"   O  0  1  N  N  N  106.707  54.130  63.039  -3.272   0.175  -0.296  "O1'"   12V  12  
12V  O1A     O1A     O  0  1  N  N  N  110.089  55.554  62.031   0.756   2.044  -2.273  O1A     12V  13  
12V  C1B     C1B     C  0  1  N  N  R  112.940  49.082  61.052   5.439  -0.049   1.201  C1B     12V  14  
12V  O1B     O1B     O  0  1  N  N  N  107.455  52.361  64.520  -2.756   2.013  -1.947  O1B     12V  15  
12V  "C2'"   "C2'"   C  0  1  N  N  R  105.849  56.356  62.468  -5.538   0.008   0.534  "C2'"   12V  16  
12V  "N2'"   "N2'"   N  0  1  N  N  N  105.901  56.692  63.893  -5.554   1.413   0.947  "N2'"   12V  17  
12V  "O2'"   "O2'"   O  0  1  N  N  N  111.067  47.612  61.036   7.064   1.419   2.288  "O2'"   12V  18  
12V  O2A     O2A     O  0  1  N  N  N  110.891  54.365  64.167  -0.008   3.653  -0.484  O2A     12V  19  
12V  C2B     C2B     C  0  1  N  N  R  111.526  48.905  61.472   6.306   1.225   1.092  C2B     12V  20  
12V  O2B     O2B     O  0  1  N  N  N  108.326  54.737  64.800  -1.870  -0.291  -2.470  O2B     12V  21  
12V  "C3'"   "C3'"   C  0  1  N  N  R  104.476  55.812  62.040  -5.046  -0.855   1.691  "C3'"   12V  22  
12V  "O3'"   "O3'"   O  0  1  N  N  N  103.414  56.662  62.531  -5.760  -0.502   2.878  "O3'"   12V  23  
12V  O3A     O3A     O  0  1  N  N  N  109.034  53.404  62.804  -0.847   1.162  -0.533  O3A     12V  24  
12V  C3B     C3B     C  0  1  N  N  S  110.928  50.075  60.661   5.278   2.365   0.912  C3B     12V  25  
12V  O3B     O3B     O  0  1  N  N  N  111.040  49.863  59.213   5.369   3.297   1.991  O3B     12V  26  
12V  "C4'"   "C4'"   C  0  1  N  N  S  104.367  55.713  60.521  -5.267  -2.335   1.394  "C4'"   12V  27  
12V  "O4'"   "O4'"   O  0  1  N  N  N  103.073  55.204  60.211  -5.034  -3.098   2.580  "O4'"   12V  28  
12V  C4B     C4B     C  0  1  N  N  R  111.923  51.170  61.002   3.911   1.644   0.934  C4B     12V  29  
12V  O4B     O4B     O  0  1  N  N  N  113.153  50.493  61.308   4.203   0.288   0.534  O4B     12V  30  
12V  "C5'"   "C5'"   C  0  1  N  N  R  105.393  54.753  59.969  -4.305  -2.797   0.297  "C5'"   12V  31  
12V  "S5'"   "S5'"   S  0  1  N  N  N  107.064  54.990  60.506  -4.674  -1.885  -1.231  "S5'"   12V  32  
12V  C5B     C5B     C  0  1  N  N  N  111.538  51.979  62.246   2.949   2.297  -0.060  C5B     12V  33  
12V  O5B     O5B     O  0  1  N  N  N  111.430  53.389  61.925   1.659   1.693   0.058  O5B     12V  34  
12V  "C6'"   "C6'"   C  0  1  N  N  N  105.742  55.075  58.525  -4.485  -4.297   0.055  "C6'"   12V  35  
12V  "O6'"   "O6'"   O  0  1  N  N  N  104.639  55.691  57.882  -5.856  -4.571  -0.240  "O6'"   12V  36  
12V  "C7'"   "C7'"   C  0  1  N  N  N  106.570  57.764  64.291  -6.390   2.283   0.346  "C7'"   12V  37  
12V  "O7'"   "O7'"   O  0  1  N  N  N  107.132  58.541  63.516  -7.130   1.902  -0.536  "O7'"   12V  38  
12V  "C8'"   "C8'"   C  0  1  N  N  N  106.593  57.967  65.805  -6.406   3.729   0.771  "C8'"   12V  39  
12V  H5      H5      H  0  1  N  N  N  115.315  48.261  64.946   7.353  -4.190   1.179  H5      12V  40  
12V  H6      H6      H  0  1  N  N  N  113.442  49.331  63.723   6.252  -2.326   2.305  H6      12V  41  
12V  "H1'"   "H1'"   H  0  1  N  N  N  107.897  55.764  62.529  -4.937   0.502  -1.478  "H1'"   12V  42  
12V  H1B     H1B     H  0  1  N  N  N  113.056  48.853  59.982   5.251  -0.293   2.247  H1B     12V  43  
12V  "H2'"   "H2'"   H  0  1  N  N  N  106.078  57.249  61.868  -6.547  -0.299   0.258  "H2'"   12V  44  
12V  "HN2'"  "HN2'"  H  0  0  N  N  N  105.434  56.115  64.562  -4.962   1.718   1.653  "HN2'"  12V  45  
12V  "HO2'"  "HO2'"  H  0  0  N  N  N  110.163  47.491  61.301   7.626   2.206   2.274  "HO2'"  12V  46  
12V  HO2A    HO2A    H  0  0  N  N  N  110.962  55.269  64.449  -0.254   3.788   0.441  HO2A    12V  47  
12V  H2B     H2B     H  0  1  N  N  N  111.394  49.062  62.553   6.967   1.165   0.228  H2B     12V  48  
12V  HO2B    HO2B    H  0  0  N  N  N  108.260  54.467  65.708  -1.500  -1.119  -2.135  HO2B    12V  49  
12V  "H3'"   "H3'"   H  0  1  N  N  N  104.360  54.803  62.462  -3.982  -0.676   1.846  "H3'"   12V  50  
12V  "HO3'"  "HO3'"  H  0  0  N  N  N  102.575  56.311  62.257  -5.500  -1.010   3.659  "HO3'"  12V  51  
12V  H3B     H3B     H  0  1  N  N  N  109.906  50.321  60.985   5.429   2.868  -0.043  H3B     12V  52  
12V  HO3B    HO3B    H  0  0  N  N  N  110.661  50.604  58.754   6.229   3.734   2.061  HO3B    12V  53  
12V  "H4'"   "H4'"   H  0  1  N  N  N  104.514  56.709  60.077  -6.294  -2.488   1.062  "H4'"   12V  54  
12V  "HO4'"  "HO4'"  H  0  0  N  N  N  102.978  55.132  59.269  -5.156  -4.050   2.465  "HO4'"  12V  55  
12V  H4B     H4B     H  0  1  N  N  N  112.046  51.846  60.143   3.489   1.661   1.939  H4B     12V  56  
12V  "H5'"   "H5'"   H  0  1  N  N  N  105.111  53.699  60.112  -3.278  -2.596   0.603  "H5'"   12V  57  
12V  H5B     H5B     H  0  1  N  N  N  110.570  51.620  62.626   2.872   3.363   0.155  H5B     12V  58  
12V  H5BA    H5BA    H  0  0  N  N  N  112.309  51.842  63.019   3.324   2.158  -1.074  H5BA    12V  59  
12V  "H6'"   "H6'"   H  0  1  N  N  N  106.604  55.758  58.503  -3.864  -4.607  -0.785  "H6'"   12V  60  
12V  "H6'A"  "H6'A"  H  0  0  N  N  N  105.998  54.145  57.997  -4.189  -4.847   0.948  "H6'A"  12V  61  
12V  "HO6'"  "HO6'"  H  0  0  N  N  N  104.867  55.888  56.981  -6.044  -5.505  -0.405  "HO6'"  12V  62  
12V  "H8'"   "H8'"   H  0  1  N  N  N  107.167  58.874  66.045  -5.680   3.881   1.570  "H8'"   12V  63  
12V  "H8'A"  "H8'A"  H  0  0  N  N  N  105.563  58.076  66.176  -6.149   4.360  -0.079  "H8'A"  12V  64  
12V  "H8'B"  "H8'B"  H  0  0  N  N  N  107.066  57.097  66.284  -7.402   3.991   1.131  "H8'B"  12V  65  
12V  HN3     HN3     H  0  1  N  N  N  116.602  46.483  61.377   7.120  -2.049  -2.392  HN3     12V  66  
#   #
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
12V  C1B    N1      SING  N  N   1  
12V  C2     N1      SING  N  N   2  
12V  N1     C6      SING  N  N   3  
12V  O2     C2      DOUB  N  N   4  
12V  C2     N3      SING  N  N   5  
12V  N3     C4      SING  N  N   6  
12V  C4     O4      DOUB  N  N   7  
12V  C4     C5      SING  N  N   8  
12V  C6     C5      DOUB  N  N   9  
12V  C5     H5      SING  N  N  10  
12V  C6     H6      SING  N  N  11  
12V  O5B    PA      SING  N  N  12  
12V  O1A    PA      DOUB  N  N  13  
12V  PA     O3A     SING  N  N  14  
12V  PA     O2A     SING  N  N  15  
12V  O3A    PB      SING  N  N  16  
12V  "O1'"  PB      SING  N  N  17  
12V  PB     O1B     DOUB  N  N  18  
12V  PB     O2B     SING  N  N  19  
12V  "S5'"  "C1'"   SING  N  N  20  
12V  "C1'"  "C2'"   SING  N  N  21  
12V  "C1'"  "O1'"   SING  N  N  22  
12V  "C1'"  "H1'"   SING  N  N  23  
12V  C1B    O4B     SING  N  N  24  
12V  C1B    C2B     SING  N  N  25  
12V  C1B    H1B     SING  N  N  26  
12V  "C3'"  "C2'"   SING  N  N  27  
12V  "C2'"  "N2'"   SING  N  N  28  
12V  "C2'"  "H2'"   SING  N  N  29  
12V  "N2'"  "C7'"   SING  N  N  30  
12V  "N2'"  "HN2'"  SING  N  N  31  
12V  "O2'"  C2B     SING  N  N  32  
12V  "O2'"  "HO2'"  SING  N  N  33  
12V  O2A    HO2A    SING  N  N  34  
12V  C3B    C2B     SING  N  N  35  
12V  C2B    H2B     SING  N  N  36  
12V  O2B    HO2B    SING  N  N  37  
12V  "C4'"  "C3'"   SING  N  N  38  
12V  "C3'"  "O3'"   SING  N  N  39  
12V  "C3'"  "H3'"   SING  N  N  40  
12V  "O3'"  "HO3'"  SING  N  N  41  
12V  O3B    C3B     SING  N  N  42  
12V  C3B    C4B     SING  N  N  43  
12V  C3B    H3B     SING  N  N  44  
12V  O3B    HO3B    SING  N  N  45  
12V  "C5'"  "C4'"   SING  N  N  46  
12V  "O4'"  "C4'"   SING  N  N  47  
12V  "C4'"  "H4'"   SING  N  N  48  
12V  "O4'"  "HO4'"  SING  N  N  49  
12V  C4B    O4B     SING  N  N  50  
12V  C4B    C5B     SING  N  N  51  
12V  C4B    H4B     SING  N  N  52  
12V  "C6'"  "C5'"   SING  N  N  53  
12V  "C5'"  "S5'"   SING  N  N  54  
12V  "C5'"  "H5'"   SING  N  N  55  
12V  O5B    C5B     SING  N  N  56  
12V  C5B    H5B     SING  N  N  57  
12V  C5B    H5BA    SING  N  N  58  
12V  "O6'"  "C6'"   SING  N  N  59  
12V  "C6'"  "H6'"   SING  N  N  60  
12V  "C6'"  "H6'A"  SING  N  N  61  
12V  "O6'"  "HO6'"  SING  N  N  62  
12V  "O7'"  "C7'"   DOUB  N  N  63  
12V  "C7'"  "C8'"   SING  N  N  64  
12V  "C8'"  "H8'"   SING  N  N  65  
12V  "C8'"  "H8'A"  SING  N  N  66  
12V  "C8'"  "H8'B"  SING  N  N  67  
12V  N3     HN3     SING  N  N  68  
#   #
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
12V  InChI             InChI                 1.03   "InChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16+/m1/s1"  
12V  InChIKey          InChI                 1.03   JPRVHSQHWXZSNC-UBDZBXRQSA-N  
12V  SMILES            ACDLabs               12.01  "O=P(OC1SC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O"  
12V  SMILES_CANONICAL  CACTVS                3.370  "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O"  
12V  SMILES            CACTVS                3.370  "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)S[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O"  
12V  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](S[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O"  
12V  SMILES            "OpenEye OEToolkits"  1.7.6  "CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)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
12V  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
12V  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)thian-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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
12V  "Create component"  2012-06-19  EBI   
12V  "Initial release"   2012-10-19  RCSB  
12V  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     12V
_pdbx_chem_comp_synonyms.name        "URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
