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                    2009-02-13 
_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 InChI            InChI                1.02b 
InChI=1/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/f/h18,25,27H 
T3F InChIKey         InChI                1.02b KVYJLJOGNUNRJK-JZLWUOJCDC 
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 
# 
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" 
# 
