data_T3F
#

_chem_comp.id                                   T3F
_chem_comp.name                                 "(3R,4S,5R,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H27 N3 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminogalactose"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-02-02
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       547.345
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    T3F
_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       3FSC
_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
T3F  O2B     O2B   O  0  1  N  N  N  31.003   0.320  58.117  -3.841  -2.837  -0.437  O2B   T3F   1  
T3F  PB      PB    P  0  1  N  N  R  31.083   1.850  57.654  -3.316  -1.523   0.333  PB    T3F   2  
T3F  O1B     O1B   O  0  1  N  N  N  29.755   2.521  57.703  -3.612  -1.646   1.778  O1B   T3F   3  
T3F  O3B     O3B   O  0  1  N  N  N  31.551   2.042  56.122  -4.058  -0.222  -0.259  O3B   T3F   4  
T3F  C1Q     C1Q   C  0  1  N  N  R  32.500   1.083  55.568  -5.464  -0.003  -0.130  C1Q   T3F   5  
T3F  O5Q     O5Q   O  0  1  N  N  N  31.753   0.257  54.692  -5.726   0.718   1.076  O5Q   T3F   6  
T3F  C5Q     C5Q   C  0  1  N  N  R  31.174   1.040  53.635  -5.072   1.986   1.151  C5Q   T3F   7  
T3F  C6Q     C6Q   C  0  1  N  N  N  30.436   0.033  52.745  -5.400   2.650   2.490  C6Q   T3F   8  
T3F  C2Q     C2Q   C  0  1  N  N  R  33.711   1.750  54.888  -5.965   0.809  -1.328  C2Q   T3F   9  
T3F  O2Q     O2Q   O  0  1  N  N  N  34.277   2.630  55.874  -5.653   0.117  -2.538  O2Q   T3F  10  
T3F  C3Q     C3Q   C  0  1  N  N  S  33.193   2.575  53.697  -5.279   2.178  -1.329  C3Q   T3F  11  
T3F  N3Q     N3Q   N  0  1  N  N  N  34.329   3.190  52.938  -5.808   2.992  -2.432  N3Q   T3F  12  
T3F  C4Q     C4Q   C  0  1  N  N  R  32.280   1.699  52.802  -5.557   2.878   0.005  C4Q   T3F  13  
T3F  O4Q     O4Q   O  0  1  N  N  N  33.075   0.634  52.249  -6.961   3.107   0.141  O4Q   T3F  14  
T3F  O3A     O3A   O  0  1  N  N  N  32.238   2.643  58.465  -1.727  -1.377   0.122  O3A   T3F  15  
T3F  PA      PA    P  0  1  N  N  R  32.168   2.781  60.084  -0.443  -2.135   0.730  PA    T3F  16  
T3F  O1A     O1A   O  0  1  N  N  N  31.058   2.054  60.804  -0.196  -1.644   2.243  O1A   T3F  17  
T3F  O2A     O2A   O  0  1  N  N  N  33.597   2.208  60.540  -0.682  -3.596   0.718  O2A   T3F  18  
T3F  "O5'"   O5*   O  0  1  N  N  N  32.224   4.371  60.340   0.853  -1.797  -0.163  O5*   T3F  19  
T3F  "C5'"   C5*   C  0  1  N  N  N  30.982   4.996  60.040   2.129  -2.401   0.057  C5*   T3F  20  
T3F  "C4'"   C4*   C  0  1  N  N  R  31.000   6.374  60.724   3.133  -1.859  -0.963  C4*   T3F  21  
T3F  "O4'"   O4*   O  0  1  N  N  N  30.976   6.248  62.186   3.379  -0.454  -0.736  O4*   T3F  22  
T3F  "C3'"   C3*   C  0  1  N  N  S  32.318   7.144  60.367   4.525  -2.507  -0.756  C3*   T3F  23  
T3F  "O3'"   O3*   O  0  1  N  N  N  32.075   8.543  60.422   4.622  -3.744  -1.466  O3*   T3F  24  
T3F  "C2'"   C2*   C  0  1  N  N  N  33.226   6.808  61.570   5.472  -1.445  -1.365  C2*   T3F  25  
T3F  "C1'"   C1*   C  0  1  N  N  R  32.205   6.718  62.767   4.643  -0.146  -1.347  C1*   T3F  26  
T3F  N1      N1    N  0  1  N  N  N  32.740   5.692  63.700   5.339   0.878  -0.562  N1    T3F  27  
T3F  C2      C2    C  0  1  N  N  N  33.552   6.073  64.740   5.536   0.688   0.755  C2    T3F  28  
T3F  O2      O2    O  0  1  N  N  N  33.819   7.258  64.939   5.135  -0.332   1.280  O2    T3F  29  
T3F  N3      N3    N  0  1  N  N  N  34.094   5.140  65.568   6.172   1.612   1.499  N3    T3F  30  
T3F  C6      C6    C  0  1  N  N  N  32.457   4.344  63.519   5.786   2.015  -1.177  C6    T3F  31  
T3F  C5      C5    C  0  1  N  N  N  32.982   3.375  64.345   6.427   2.958  -0.454  C5    T3F  32  
T3F  C5M     C5M   C  0  1  N  N  N  32.646   1.910  64.103   6.926   4.218  -1.114  C5M   T3F  33  
T3F  C4      C4    C  0  1  N  N  N  33.859   3.798  65.413   6.624   2.748   0.932  C4    T3F  34  
T3F  O4      O4    O  0  1  N  N  N  34.402   3.004  66.196   7.199   3.585   1.605  O4    T3F  35  
T3F  HO2B    HO2B  H  0  0  N  N  N  30.987  -0.243  57.352  -3.680  -2.825  -1.390  HO2B  T3F  36  
T3F  H1Q     H1Q   H  0  1  N  N  N  32.961   0.486  56.368  -5.981  -0.962  -0.100  H1Q   T3F  37  
T3F  H5Q     H5Q   H  0  1  N  N  N  30.517   1.828  54.032  -3.994   1.844   1.070  H5Q   T3F  38  
T3F  H6Q     H6Q   H  0  1  N  N  N  30.259   0.479  51.755  -5.055   2.015   3.305  H6Q   T3F  39  
T3F  H6QA    H6QA  H  0  0  N  N  N  31.047  -0.875  52.635  -4.901   3.618   2.547  H6QA  T3F  40  
T3F  H6QB    H6QB  H  0  0  N  N  N  29.472  -0.227  53.207  -6.478   2.792   2.570  H6QB  T3F  41  
T3F  H2Q     H2Q   H  0  1  N  N  N  34.453   1.022  54.529  -7.045   0.941  -1.252  H2Q   T3F  42  
T3F  HO2Q    HO2Q  H  0  0  N  N  N  34.402   2.156  56.688  -6.051  -0.762  -2.603  HO2Q  T3F  43  
T3F  H3Q     H3Q   H  0  1  N  N  N  32.582   3.410  54.071  -4.204   2.048  -1.455  H3Q   T3F  44  
T3F  HN3Q    HN3Q  H  0  0  N  N  N  34.058   3.327  51.985  -5.642   2.546  -3.322  HN3Q  T3F  45  
T3F  HN3A    HN3A  H  0  0  N  N  N  34.565   4.071  53.347  -6.790   3.183  -2.302  HN3A  T3F  46  
T3F  H4Q     H4Q   H  0  1  N  N  N  31.836   2.337  52.024  -5.027   3.830   0.035  H4Q   T3F  47  
T3F  HO4Q    HO4Q  H  0  0  N  N  N  33.250   0.812  51.332  -7.210   3.544   0.967  HO4Q  T3F  48  
T3F  HO1A    HO1A  H  0  0  N  N  N  31.312   1.901  61.707  -0.032  -0.695   2.326  HO1A  T3F  49  
T3F  "H5'"   H5*   H  0  1  N  N  N  30.864   5.110  58.952   2.473  -2.168   1.065  H5*   T3F  50  
T3F  "H5'A"  H5*A  H  0  0  N  N  N  30.139   4.389  60.401   2.044  -3.482  -0.057  H5*A  T3F  51  
T3F  "H4'"   H4*   H  0  1  N  N  N  30.109   6.912  60.369   2.775  -2.027  -1.978  H4*   T3F  52  
T3F  "H3'"   H3*   H  0  1  N  N  N  32.719   6.883  59.377   4.734  -2.652   0.304  H3*   T3F  53  
T3F  "HO3'"  HO3*  H  0  0  N  N  N  32.021   8.820  61.329   5.476  -4.188  -1.368  HO3*  T3F  54  
T3F  "H2'"   H2*   H  0  1  N  N  N  33.764   5.860  61.422   6.367  -1.335  -0.753  H2*   T3F  55  
T3F  "H2'A"  H2*A  H  0  0  N  N  N  34.019   7.553  61.734   5.739  -1.712  -2.388  H2*A  T3F  56  
T3F  "H1'"   H1*   H  0  1  N  N  N  32.053   7.669  63.298   4.486   0.208  -2.365  H1*   T3F  57  
T3F  HN3     HN3   H  0  1  N  N  N  34.684   5.443  66.316   6.306   1.459   2.448  HN3   T3F  58  
T3F  H6      H6    H  0  1  N  N  N  31.808   4.048  62.708   5.628   2.158  -2.236  H6    T3F  59  
T3F  H5M     H5M   H  0  1  N  N  N  32.565   1.726  63.022   6.149   4.981  -1.076  H5M   T3F  60  
T3F  H5MA    H5MA  H  0  0  N  N  N  33.441   1.277  64.524   7.813   4.576  -0.590  H5MA  T3F  61  
T3F  H5MB    H5MB  H  0  0  N  N  N  31.689   1.669  64.589   7.179   4.008  -2.154  H5MB  T3F  62  
#   #
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
T3F  PB     O2B     SING  N  N   1  
T3F  O2B    HO2B    SING  N  N   2  
T3F  O3B    PB      SING  N  N   3  
T3F  PB     O1B     DOUB  N  N   4  
T3F  PB     O3A     SING  N  N   5  
T3F  C1Q    O3B     SING  N  N   6  
T3F  O5Q    C1Q     SING  N  N   7  
T3F  C2Q    C1Q     SING  N  N   8  
T3F  C1Q    H1Q     SING  N  N   9  
T3F  C5Q    O5Q     SING  N  N  10  
T3F  C6Q    C5Q     SING  N  N  11  
T3F  C4Q    C5Q     SING  N  N  12  
T3F  C5Q    H5Q     SING  N  N  13  
T3F  C6Q    H6Q     SING  N  N  14  
T3F  C6Q    H6QA    SING  N  N  15  
T3F  C6Q    H6QB    SING  N  N  16  
T3F  C3Q    C2Q     SING  N  N  17  
T3F  C2Q    O2Q     SING  N  N  18  
T3F  C2Q    H2Q     SING  N  N  19  
T3F  O2Q    HO2Q    SING  N  N  20  
T3F  C4Q    C3Q     SING  N  N  21  
T3F  N3Q    C3Q     SING  N  N  22  
T3F  C3Q    H3Q     SING  N  N  23  
T3F  N3Q    HN3Q    SING  N  N  24  
T3F  N3Q    HN3A    SING  N  N  25  
T3F  O4Q    C4Q     SING  N  N  26  
T3F  C4Q    H4Q     SING  N  N  27  
T3F  O4Q    HO4Q    SING  N  N  28  
T3F  O3A    PA      SING  N  N  29  
T3F  PA     "O5'"   SING  N  N  30  
T3F  PA     O2A     DOUB  N  N  31  
T3F  PA     O1A     SING  N  N  32  
T3F  O1A    HO1A    SING  N  N  33  
T3F  "C5'"  "O5'"   SING  N  N  34  
T3F  "C5'"  "C4'"   SING  N  N  35  
T3F  "C5'"  "H5'"   SING  N  N  36  
T3F  "C5'"  "H5'A"  SING  N  N  37  
T3F  "C3'"  "C4'"   SING  N  N  38  
T3F  "C4'"  "O4'"   SING  N  N  39  
T3F  "C4'"  "H4'"   SING  N  N  40  
T3F  "O4'"  "C1'"   SING  N  N  41  
T3F  "C3'"  "O3'"   SING  N  N  42  
T3F  "C3'"  "C2'"   SING  N  N  43  
T3F  "C3'"  "H3'"   SING  N  N  44  
T3F  "O3'"  "HO3'"  SING  N  N  45  
T3F  "C2'"  "C1'"   SING  N  N  46  
T3F  "C2'"  "H2'"   SING  N  N  47  
T3F  "C2'"  "H2'A"  SING  N  N  48  
T3F  "C1'"  N1      SING  N  N  49  
T3F  "C1'"  "H1'"   SING  N  N  50  
T3F  C6     N1      SING  N  N  51  
T3F  N1     C2      SING  N  N  52  
T3F  C2     O2      DOUB  N  N  53  
T3F  C2     N3      SING  N  N  54  
T3F  C4     N3      SING  N  N  55  
T3F  N3     HN3     SING  N  N  56  
T3F  C6     C5      DOUB  N  N  57  
T3F  C6     H6      SING  N  N  58  
T3F  C5M    C5      SING  N  N  59  
T3F  C5     C4      SING  N  N  60  
T3F  C5M    H5M     SING  N  N  61  
T3F  C5M    H5MA    SING  N  N  62  
T3F  C5M    H5MB    SING  N  N  63  
T3F  C4     O4      DOUB  N  N  64  
#   #
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
T3F  SMILES            ACDLabs               10.04  "O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O"  
T3F  SMILES_CANONICAL  CACTVS                3.341  "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](N)[C@H]1O"  
T3F  SMILES            CACTVS                3.341  "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](N)[CH]1O"  
T3F  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O"  
T3F  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O"  
T3F  InChI             InChI                 1.03   "InChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12+,13-,15-/m1/s1"  
T3F  InChIKey          InChI                 1.03   KVYJLJOGNUNRJK-FQLHZTMTSA-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
T3F  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2R,3R,4S,5R,6R)-4-amino-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
T3F  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3R,4S,5R,6R)-4-amino-3,5-dihydroxy-6-methyl-oxan-2-yl] [hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]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
T3F  "Create component"   2009-02-02  RCSB  
T3F  "Modify descriptor"  2011-06-04  RCSB  
T3F  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     T3F
_pdbx_chem_comp_synonyms.name        "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminogalactose"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
