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 ? ##