data_T3Q # _chem_comp.id T3Q _chem_comp.name "[(3R,4S,5S,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-aminoglucose" _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 T3Q _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 3FSB _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 T3Q O4 O4 O 0 1 N N N 46.489 -8.906 -13.157 -7.027 -3.605 1.645 O4 T3Q 1 T3Q C4 C4 C 0 1 N N N 45.506 -9.114 -12.399 -6.480 -2.745 0.978 C4 T3Q 2 T3Q N3 N3 N 0 1 N N N 44.691 -10.213 -12.584 -6.067 -1.598 1.554 N3 T3Q 3 T3Q C2 C2 C 0 1 N N N 43.647 -10.401 -11.729 -5.463 -0.647 0.817 C2 T3Q 4 T3Q O2 O2 O 0 1 N N N 42.941 -11.373 -11.857 -5.095 0.382 1.350 O2 T3Q 5 T3Q C5 C5 C 0 1 N N N 45.207 -8.209 -11.323 -6.268 -2.942 -0.408 C5 T3Q 6 T3Q C5M C5M C 0 1 N N N 46.083 -7.009 -11.091 -6.715 -4.216 -1.075 C5M T3Q 7 T3Q C6 C6 C 0 1 N N N 44.145 -8.425 -10.501 -5.660 -1.972 -1.123 C6 T3Q 8 T3Q N1 N1 N 0 1 N N N 43.358 -9.549 -10.712 -5.259 -0.820 -0.502 N1 T3Q 9 T3Q "C1'" C1* C 0 1 N N R 42.208 -9.858 -9.821 -4.599 0.232 -1.278 C1* T3Q 10 T3Q "O4'" O4* O 0 1 N N N 41.717 -8.666 -9.169 -3.338 0.588 -0.671 O4* T3Q 11 T3Q "C2'" C2* C 0 1 N N N 42.676 -10.794 -8.673 -5.435 1.531 -1.243 C2* T3Q 12 T3Q "C3'" C3* C 0 1 N N S 41.817 -10.360 -7.447 -4.378 2.656 -1.178 C3* T3Q 13 T3Q "O3'" O3* O 0 1 N N N 40.594 -11.109 -7.365 -4.480 3.506 -2.323 O3* T3Q 14 T3Q "C4'" C4* C 0 1 N N R 41.516 -8.858 -7.716 -3.029 1.903 -1.181 C4* T3Q 15 T3Q "C5'" C5* C 0 1 N N N 42.527 -7.965 -6.976 -2.024 2.607 -0.266 C5* T3Q 16 T3Q "O5'" O5* O 0 1 N N N 43.868 -8.290 -7.386 -0.772 1.921 -0.317 O5* T3Q 17 T3Q PA PA P 0 1 N N S 44.956 -7.154 -6.906 0.518 2.388 0.526 PA T3Q 18 T3Q O1A O1A O 0 1 N N N 44.609 -5.807 -7.462 0.165 2.476 1.961 O1A T3Q 19 T3Q O2A O2A O 0 1 N N N 46.381 -7.695 -7.446 1.007 3.830 0.004 O2A T3Q 20 T3Q O3A O3A O 0 1 N N N 45.094 -7.090 -5.303 1.704 1.316 0.330 O3A T3Q 21 T3Q PB PB P 0 1 N N S 44.890 -5.637 -4.582 3.037 0.959 1.159 PB T3Q 22 T3Q O1B O1B O 0 1 N N N 43.557 -5.029 -4.815 2.655 0.031 2.418 O1B T3Q 23 T3Q O2B O2B O 0 1 N N N 46.012 -4.521 -4.895 3.667 2.209 1.641 O2B T3Q 24 T3Q O3B O3B O 0 1 N N N 45.014 -6.128 -3.071 4.067 0.172 0.205 O3B T3Q 25 T3Q O4Q O4Q O 0 1 N N N 45.290 -6.381 1.445 5.243 -3.625 -1.757 O4Q T3Q 26 T3Q C4Q C4Q C 0 1 N N S 46.129 -6.456 0.275 5.768 -2.636 -0.869 C4Q T3Q 27 T3Q C5Q C5Q C 0 1 N N R 45.980 -5.203 -0.627 4.863 -2.518 0.359 C5Q T3Q 28 T3Q O5Q O5Q O 0 1 N N N 46.863 -5.320 -1.759 5.358 -1.488 1.217 O5Q T3Q 29 T3Q C6Q C6Q C 0 1 N N N 46.359 -3.920 0.137 4.851 -3.849 1.114 C6Q T3Q 30 T3Q C3Q C3Q C 0 1 N N S 45.707 -7.665 -0.555 5.824 -1.283 -1.586 C3Q T3Q 31 T3Q N3Q N3Q N 0 1 N N N 45.807 -8.888 0.260 6.750 -1.367 -2.723 N3Q T3Q 32 T3Q C2Q C2Q C 0 1 N N R 46.585 -7.709 -1.823 6.314 -0.216 -0.603 C2Q T3Q 33 T3Q O2Q O2Q O 0 1 N N N 46.235 -8.799 -2.670 6.303 1.062 -1.240 O2Q T3Q 34 T3Q C1Q C1Q C 0 1 N N R 46.412 -6.387 -2.595 5.387 -0.192 0.616 C1Q T3Q 35 T3Q HN3 HN3 H 0 1 N N N 44.863 -10.857 -13.329 -6.206 -1.457 2.504 HN3 T3Q 36 T3Q H5M H5M H 0 1 N N N 46.297 -6.913 -10.016 -7.181 -4.869 -0.337 H5M T3Q 37 T3Q H5MA H5MA H 0 0 N N N 47.027 -7.132 -11.643 -7.436 -3.983 -1.859 H5MA T3Q 38 T3Q H5MB H5MB H 0 0 N N N 45.566 -6.104 -11.444 -5.853 -4.720 -1.512 H5MB T3Q 39 T3Q H6 H6 H 0 1 N N N 43.919 -7.736 -9.701 -5.489 -2.105 -2.182 H6 T3Q 40 T3Q "H1'" H1* H 0 1 N N N 41.428 -10.315 -10.448 -4.446 -0.096 -2.307 H1* T3Q 41 T3Q "H2'" H2* H 0 1 N N N 42.504 -11.851 -8.926 -6.035 1.623 -2.148 H2* T3Q 42 T3Q "H2'A" H2*A H 0 0 N N N 43.755 -10.709 -8.478 -6.071 1.552 -0.358 H2*A T3Q 43 T3Q "H3'" H3* H 0 1 N N N 42.338 -10.535 -6.494 -4.492 3.235 -0.262 H3* T3Q 44 T3Q "HO3'" HO3* H 0 0 N N N 40.384 -11.274 -6.453 -5.332 3.957 -2.403 HO3* T3Q 45 T3Q "H4'" H4* H 0 1 N N N 40.502 -8.595 -7.379 -2.635 1.834 -2.196 H4* T3Q 46 T3Q "H5'" H5* H 0 1 N N N 42.321 -6.911 -7.213 -1.888 3.636 -0.599 H5* T3Q 47 T3Q "H5'A" H5*A H 0 0 N N N 42.431 -8.133 -5.893 -2.400 2.603 0.757 H5*A T3Q 48 T3Q HO2A HO2A H 0 0 N N N 46.343 -7.801 -8.389 1.255 3.847 -0.930 HO2A T3Q 49 T3Q HO1B HO1B H 0 0 N N N 43.118 -4.899 -3.983 2.236 -0.807 2.176 HO1B T3Q 50 T3Q HO4Q HO4Q H 0 0 N N N 45.833 -6.365 2.224 5.177 -4.508 -1.367 HO4Q T3Q 51 T3Q H4Q H4Q H 0 1 N N N 47.172 -6.530 0.618 6.772 -2.924 -0.556 H4Q T3Q 52 T3Q H5Q H5Q H 0 1 N N N 44.930 -5.141 -0.948 3.849 -2.271 0.042 H5Q T3Q 53 T3Q H6Q H6Q H 0 1 N N N 46.449 -4.145 1.210 5.864 -4.095 1.432 H6Q T3Q 54 T3Q H6QA H6QA H 0 0 N N N 47.320 -3.539 -0.240 4.206 -3.765 1.989 H6QA T3Q 55 T3Q H6QB H6QB H 0 0 N N N 45.578 -3.160 -0.014 4.474 -4.635 0.459 H6QB T3Q 56 T3Q H3Q H3Q H 0 1 N N N 44.656 -7.589 -0.872 4.829 -1.020 -1.945 H3Q T3Q 57 T3Q HN3Q HN3Q H 0 0 N N N 45.830 -9.688 -0.340 6.804 -0.486 -3.212 HN3Q T3Q 58 T3Q HN3A HN3A H 0 0 N N N 46.644 -8.857 0.806 7.665 -1.670 -2.422 HN3A T3Q 59 T3Q H2Q H2Q H 0 1 N N N 47.632 -7.846 -1.514 7.329 -0.455 -0.283 H2Q T3Q 60 T3Q HO2Q HO2Q H 0 0 N N N 46.157 -8.492 -3.566 6.602 1.787 -0.674 HO2Q T3Q 61 T3Q H1Q H1Q H 0 1 N N N 47.014 -6.460 -3.513 5.755 0.536 1.339 H1Q T3Q 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 T3Q O4 C4 DOUB N N 1 T3Q N3 C4 SING N N 2 T3Q C4 C5 SING N N 3 T3Q N3 C2 SING N N 4 T3Q N3 HN3 SING N N 5 T3Q O2 C2 DOUB N N 6 T3Q C2 N1 SING N N 7 T3Q C5 C5M SING N N 8 T3Q C5 C6 DOUB N N 9 T3Q C5M H5M SING N N 10 T3Q C5M H5MA SING N N 11 T3Q C5M H5MB SING N N 12 T3Q N1 C6 SING N N 13 T3Q C6 H6 SING N N 14 T3Q N1 "C1'" SING N N 15 T3Q "C1'" "O4'" SING N N 16 T3Q "C1'" "C2'" SING N N 17 T3Q "C1'" "H1'" SING N N 18 T3Q "O4'" "C4'" SING N N 19 T3Q "C2'" "C3'" SING N N 20 T3Q "C2'" "H2'" SING N N 21 T3Q "C2'" "H2'A" SING N N 22 T3Q "C4'" "C3'" SING N N 23 T3Q "C3'" "O3'" SING N N 24 T3Q "C3'" "H3'" SING N N 25 T3Q "O3'" "HO3'" SING N N 26 T3Q "C4'" "C5'" SING N N 27 T3Q "C4'" "H4'" SING N N 28 T3Q "O5'" "C5'" SING N N 29 T3Q "C5'" "H5'" SING N N 30 T3Q "C5'" "H5'A" SING N N 31 T3Q "O5'" PA SING N N 32 T3Q O1A PA DOUB N N 33 T3Q O2A PA SING N N 34 T3Q PA O3A SING N N 35 T3Q O2A HO2A SING N N 36 T3Q O3A PB SING N N 37 T3Q O2B PB DOUB N N 38 T3Q O1B PB SING N N 39 T3Q PB O3B SING N N 40 T3Q O1B HO1B SING N N 41 T3Q O3B C1Q SING N N 42 T3Q C4Q O4Q SING N N 43 T3Q O4Q HO4Q SING N N 44 T3Q C5Q C4Q SING N N 45 T3Q C3Q C4Q SING N N 46 T3Q C4Q H4Q SING N N 47 T3Q O5Q C5Q SING N N 48 T3Q C5Q C6Q SING N N 49 T3Q C5Q H5Q SING N N 50 T3Q C1Q O5Q SING N N 51 T3Q C6Q H6Q SING N N 52 T3Q C6Q H6QA SING N N 53 T3Q C6Q H6QB SING N N 54 T3Q C2Q C3Q SING N N 55 T3Q C3Q N3Q SING N N 56 T3Q C3Q H3Q SING N N 57 T3Q N3Q HN3Q SING N N 58 T3Q N3Q HN3A SING N N 59 T3Q O2Q C2Q SING N N 60 T3Q C1Q C2Q SING N N 61 T3Q C2Q H2Q SING N N 62 T3Q O2Q HO2Q SING N N 63 T3Q C1Q H1Q SING 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 T3Q 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" T3Q 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" T3Q 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" T3Q 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" T3Q 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" T3Q 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" T3Q InChIKey InChI 1.03 KVYJLJOGNUNRJK-HALQBZCBSA-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 T3Q "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4S,5S,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)" T3Q "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyl-oxan-2-yl]oxy-hydroxy-phosphoryl] [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl 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 T3Q "Create component" 2009-02-02 RCSB T3Q "Modify descriptor" 2011-06-04 RCSB T3Q "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id T3Q _pdbx_chem_comp_synonyms.name "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##