data_1JB # _chem_comp.id 1JB _chem_comp.name ;[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate ; _chem_comp.type SACCHARIDE _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 N2 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms dTDP-fucose _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-02-14 _chem_comp.pdbx_modified_date 2020-06-17 _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 548.330 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1JB _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 4J7G _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 1JB N1 N1 N 0 1 N N N -29.832 15.066 -13.979 -5.345 0.882 0.560 N1 1JB 1 1JB N3 N3 N 0 1 N N N -29.936 14.771 -11.704 -6.183 1.608 -1.503 N3 1JB 2 1JB C4 C4 C 0 1 N N N -30.453 13.532 -11.847 -6.638 2.744 -0.937 C4 1JB 3 1JB C5 C5 C 0 1 N N N -30.687 13.021 -13.120 -6.436 2.961 0.447 C5 1JB 4 1JB C6 C6 C 0 1 N N N -30.323 13.831 -14.184 -5.790 2.021 1.172 C6 1JB 5 1JB O1B O1B O 0 1 N N N -33.103 13.964 -20.823 3.602 -1.660 -1.779 O1B 1JB 6 1JB PB PB P 0 1 N N N -33.899 13.109 -19.889 3.307 -1.532 -0.334 PB 1JB 7 1JB O2B O2B O 0 1 N N N -35.262 13.543 -19.505 3.831 -2.844 0.438 O2B 1JB 8 1JB O3B O3B O 0 1 N N N -33.900 11.634 -20.597 4.050 -0.230 0.253 O3B 1JB 9 1JB C1Q C1Q C 0 1 N N R -34.793 10.636 -20.112 5.457 -0.013 0.123 C1Q 1JB 10 1JB O5Q O5Q O 0 1 N N N -35.906 10.758 -21.008 5.719 0.704 -1.086 O5Q 1JB 11 1JB C5Q C5Q C 0 1 N N R -35.766 10.453 -22.387 5.066 1.973 -1.164 C5Q 1JB 12 1JB C6Q C6Q C 0 1 N N N -36.988 10.886 -23.199 5.394 2.633 -2.505 C6Q 1JB 13 1JB C4Q C4Q C 0 1 N N R -35.009 9.197 -22.782 5.553 2.868 -0.022 C4Q 1JB 14 1JB O4Q O4Q O 0 1 N N N -36.008 8.267 -22.402 6.957 3.095 -0.159 O4Q 1JB 15 1JB C3Q C3Q C 0 1 N N S -33.847 9.103 -21.800 5.275 2.172 1.315 C3Q 1JB 16 1JB O3Q O3Q O 0 1 N N N -33.128 7.926 -22.179 5.793 2.967 2.384 O3Q 1JB 17 1JB C2Q C2Q C 0 1 N N R -34.169 9.253 -20.331 5.960 0.802 1.317 C2Q 1JB 18 1JB O2Q O2Q O 0 1 N N N -32.907 9.134 -19.642 5.647 0.114 2.530 O2Q 1JB 19 1JB O3A O3A O 0 1 N N N -33.340 12.977 -18.369 1.718 -1.383 -0.123 O3A 1JB 20 1JB PA PA P 0 1 N N N -31.865 12.525 -18.017 0.433 -2.142 -0.727 PA 1JB 21 1JB O1A O1A O 0 1 N N N -31.795 11.383 -17.055 0.185 -1.655 -2.242 O1A 1JB 22 1JB O2A O2A O 0 1 N N N -31.211 12.180 -19.338 0.670 -3.603 -0.712 O2A 1JB 23 1JB O5X O5X O 0 1 N N N -31.168 13.909 -17.549 -0.862 -1.799 0.165 O5X 1JB 24 1JB C5X C5X C 0 1 N N N -31.519 15.278 -17.762 -2.139 -2.403 -0.052 C5X 1JB 25 1JB C4X C4X C 0 1 N N R -30.331 16.060 -17.206 -3.142 -1.856 0.966 C4X 1JB 26 1JB O4X O4X O 0 1 N N N -30.610 16.251 -15.822 -3.386 -0.452 0.736 O4X 1JB 27 1JB C3X C3X C 0 1 N N S -29.115 15.151 -17.247 -4.535 -2.504 0.763 C3X 1JB 28 1JB O3X O3X O 0 1 N N N -28.182 15.688 -18.179 -4.633 -3.738 1.477 O3X 1JB 29 1JB C2X C2X C 0 1 N N N -28.397 15.259 -15.912 -5.480 -1.438 1.370 C2X 1JB 30 1JB C1X C1X C 0 1 N N R -29.444 15.962 -15.056 -4.650 -0.140 1.347 C1X 1JB 31 1JB C2 C2 C 0 1 N N N -29.595 15.544 -12.748 -5.543 0.688 -0.757 C2 1JB 32 1JB O2 O2 O 0 1 N N N -29.114 16.696 -12.623 -5.138 -0.332 -1.281 O2 1JB 33 1JB C5M C5M C 0 1 N N N -31.277 11.648 -13.336 -6.935 4.222 1.104 C5M 1JB 34 1JB O4 O4 O 0 1 N N N -30.753 12.850 -10.849 -7.218 3.577 -1.611 O4 1JB 35 1JB H1 H1 H 0 1 N N N -29.801 15.129 -10.780 -6.318 1.452 -2.450 H1 1JB 36 1JB H2 H2 H 0 1 N N N -30.435 13.465 -15.194 -5.627 2.169 2.229 H2 1JB 37 1JB H3 H3 H 0 1 N N N -35.465 14.366 -19.933 3.670 -2.829 1.392 H3 1JB 38 1JB H4 H4 H 0 1 N N N -35.074 10.785 -19.059 5.972 -0.973 0.095 H4 1JB 39 1JB H5 H5 H 0 1 N N N -35.044 11.222 -22.699 3.988 1.833 -1.082 H5 1JB 40 1JB H6 H6 H 0 1 N N N -37.405 11.809 -22.771 5.048 1.995 -3.318 H6 1JB 41 1JB H7 H7 H 0 1 N N N -36.689 11.068 -24.242 4.896 3.601 -2.565 H7 1JB 42 1JB H8 H8 H 0 1 N N N -37.749 10.092 -23.168 6.472 2.773 -2.587 H8 1JB 43 1JB H9 H9 H 0 1 N N N -34.704 9.171 -23.839 5.025 3.820 -0.054 H9 1JB 44 1JB H10 H10 H 0 1 N N N -35.705 7.385 -22.581 7.206 3.529 -0.986 H10 1JB 45 1JB H11 H11 H 0 1 N N N -33.194 9.954 -22.043 4.200 2.043 1.442 H11 1JB 46 1JB H12 H12 H 0 1 N N N -32.384 7.809 -21.600 5.652 2.586 3.261 H12 1JB 47 1JB H13 H13 H 0 1 N N N -34.872 8.469 -20.013 7.039 0.934 1.240 H13 1JB 48 1JB H14 H14 H 0 1 N N N -33.047 9.221 -18.706 6.049 -0.763 2.600 H14 1JB 49 1JB H15 H15 H 0 1 N N N -31.348 10.651 -17.464 0.023 -0.706 -2.328 H15 1JB 50 1JB H16 H16 H 0 1 N N N -31.654 15.484 -18.834 -2.484 -2.172 -1.060 H16 1JB 51 1JB H17 H17 H 0 1 N N N -32.442 15.533 -17.220 -2.055 -3.483 0.065 H17 1JB 52 1JB H18 H18 H 0 1 N N N -30.164 16.998 -17.755 -2.784 -2.022 1.983 H18 1JB 53 1JB H19 H19 H 0 1 N N N -29.396 14.111 -17.470 -4.744 -2.651 -0.297 H19 1JB 54 1JB H20 H20 H 0 1 N N N -27.414 15.130 -18.216 -5.487 -4.181 1.380 H20 1JB 55 1JB H21 H21 H 0 1 N N N -28.149 14.266 -15.508 -6.375 -1.329 0.757 H21 1JB 56 1JB H22 H22 H 0 1 N N N -27.479 15.860 -15.997 -5.746 -1.703 2.393 H22 1JB 57 1JB H23 H23 H 0 1 N N N -29.013 16.886 -14.644 -4.492 0.217 2.364 H23 1JB 58 1JB H24 H24 H 0 1 N N N -31.491 11.183 -12.362 -7.426 4.849 0.360 H24 1JB 59 1JB H25 H25 H 0 1 N N N -32.210 11.736 -13.913 -7.646 3.966 1.890 H25 1JB 60 1JB H26 H26 H 0 1 N N N -30.561 11.024 -13.891 -6.094 4.763 1.538 H26 1JB 61 # # 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 1JB C6Q C5Q SING N N 1 1JB C4Q O4Q SING N N 2 1JB C4Q C5Q SING N N 3 1JB C4Q C3Q SING N N 4 1JB C5Q O5Q SING N N 5 1JB O3Q C3Q SING N N 6 1JB C3Q C2Q SING N N 7 1JB O5Q C1Q SING N N 8 1JB O1B PB DOUB N N 9 1JB O3B C1Q SING N N 10 1JB O3B PB SING N N 11 1JB C2Q C1Q SING N N 12 1JB C2Q O2Q SING N N 13 1JB PB O2B SING N N 14 1JB PB O3A SING N N 15 1JB O2A PA DOUB N N 16 1JB O3A PA SING N N 17 1JB O3X C3X SING N N 18 1JB PA O5X SING N N 19 1JB PA O1A SING N N 20 1JB C5X O5X SING N N 21 1JB C5X C4X SING N N 22 1JB C3X C4X SING N N 23 1JB C3X C2X SING N N 24 1JB C4X O4X SING N N 25 1JB C2X C1X SING N N 26 1JB O4X C1X SING N N 27 1JB C1X N1 SING N N 28 1JB C6 N1 SING N N 29 1JB C6 C5 DOUB N N 30 1JB N1 C2 SING N N 31 1JB C5M C5 SING N N 32 1JB C5 C4 SING N N 33 1JB C2 O2 DOUB N N 34 1JB C2 N3 SING N N 35 1JB C4 N3 SING N N 36 1JB C4 O4 DOUB N N 37 1JB N3 H1 SING N N 38 1JB C6 H2 SING N N 39 1JB O2B H3 SING N N 40 1JB C1Q H4 SING N N 41 1JB C5Q H5 SING N N 42 1JB C6Q H6 SING N N 43 1JB C6Q H7 SING N N 44 1JB C6Q H8 SING N N 45 1JB C4Q H9 SING N N 46 1JB O4Q H10 SING N N 47 1JB C3Q H11 SING N N 48 1JB O3Q H12 SING N N 49 1JB C2Q H13 SING N N 50 1JB O2Q H14 SING N N 51 1JB O1A H15 SING N N 52 1JB C5X H16 SING N N 53 1JB C5X H17 SING N N 54 1JB C4X H18 SING N N 55 1JB C3X H19 SING N N 56 1JB O3X H20 SING N N 57 1JB C2X H21 SING N N 58 1JB C2X H22 SING N N 59 1JB C1X H23 SING N N 60 1JB C5M H24 SING N N 61 1JB C5M H25 SING N N 62 1JB C5M H26 SING N N 63 # # 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 1JB SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)C)O)O)C" 1JB InChI InChI 1.03 "InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8+,9-,10-,11+,12+,13-,15-/m1/s1" 1JB InChIKey InChI 1.03 ZOSQFDVXNQFKBY-FQLHZTMTSA-N 1JB SMILES_CANONICAL CACTVS 3.370 "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](O)[C@H]1O" 1JB SMILES CACTVS 3.370 "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](O)[CH]1O" 1JB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O" 1JB SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)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 1JB "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" 1JB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] 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 1JB "Create component" 2013-02-14 RCSB 1JB "Initial release" 2013-05-22 RCSB 1JB "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 1JB _pdbx_chem_comp_synonyms.name dTDP-fucose _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##