data_TDX # _chem_comp.id TDX _chem_comp.name "THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H24 N2 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-11-23 _chem_comp.pdbx_modified_date 2011-06-04 _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 534.303 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TDX _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1KEP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 TDX O4 O4 O 0 1 N N N -20.770 -11.286 72.139 3.417 -1.244 -7.574 O4 TDX 1 TDX C4 C4 C 0 1 N N N -20.925 -10.052 72.244 2.512 -0.683 -6.982 C4 TDX 2 TDX N3 N3 N 0 1 N N N -21.942 -9.520 72.946 1.638 -1.396 -6.244 N3 TDX 3 TDX C2 C2 C 0 1 N N N -22.093 -8.214 73.042 0.638 -0.775 -5.591 C2 TDX 4 TDX O2 O2 O 0 1 N N N -23.080 -7.789 73.721 -0.145 -1.431 -4.932 O2 TDX 5 TDX C5 C5 C 0 1 N N N -20.005 -9.162 71.558 2.374 0.723 -7.057 C5 TDX 6 TDX C5M C5M C 0 1 N N N -18.858 -9.722 70.738 3.340 1.543 -7.872 C5M TDX 7 TDX C6 C6 C 0 1 N N N -20.225 -7.828 71.652 1.362 1.320 -6.392 C6 TDX 8 TDX N1 N1 N 0 1 N N N -21.234 -7.378 72.420 0.493 0.560 -5.657 N1 TDX 9 TDX C1B C1* C 0 1 N N R -21.459 -5.943 72.500 -0.605 1.207 -4.935 C1B TDX 10 TDX C2B C2* C 0 1 N N N -20.243 -5.063 72.794 -1.955 0.657 -5.434 C2B TDX 11 TDX C3B C3* C 0 1 N N S -20.580 -3.791 72.001 -2.619 0.073 -4.164 C3B TDX 12 TDX O3B O3* O 0 1 N N N -21.390 -2.833 72.760 -4.015 0.379 -4.131 O3B TDX 13 TDX O4B O4* O 0 1 N N N -21.989 -5.542 71.219 -0.511 0.910 -3.532 O4B TDX 14 TDX C4B C4* C 0 1 N N R -21.433 -4.293 70.814 -1.864 0.815 -3.032 C4B TDX 15 TDX C5B C5* C 0 1 N N N -20.577 -4.457 69.570 -1.907 0.005 -1.734 C5B TDX 16 TDX O5B O5* O 0 1 N N N -19.416 -5.204 69.920 -1.204 0.710 -0.709 O5B TDX 17 TDX PA PA P 0 1 N N S -18.205 -5.389 68.872 -1.290 -0.193 0.619 PA TDX 18 TDX O1A O1A O 0 1 N N N -18.671 -6.235 67.713 -0.662 -1.509 0.362 O1A TDX 19 TDX O2A O2A O 0 1 N N N -17.031 -5.897 69.662 -2.833 -0.405 1.026 O2A TDX 20 TDX O3A O3A O 0 1 N N N -17.969 -3.955 68.184 -0.514 0.544 1.821 O3A TDX 21 TDX PB PB P 0 1 N N R -17.446 -2.563 68.844 -0.639 -0.410 3.112 PB TDX 22 TDX O1B O1B O 0 1 N N N -16.700 -2.712 70.140 -0.022 -1.722 2.816 O1B TDX 23 TDX O2B O2B O 0 1 N N N -18.600 -1.652 68.885 -2.193 -0.618 3.477 O2B TDX 24 TDX "O1'" "O1'" O 0 1 N N N -16.425 -2.104 67.685 0.118 0.270 4.358 "O1'" TDX 25 TDX "C1'" "C1'" C 0 1 N N R -16.783 -2.340 66.319 -0.027 -0.620 5.466 "C1'" TDX 26 TDX "O5'" "O5'" O 0 1 N N N -17.192 -1.108 65.753 1.061 -1.541 5.481 "O5'" TDX 27 TDX "C5'" "C5'" C 0 1 N N N -16.178 -0.077 65.824 2.268 -0.783 5.427 "C5'" TDX 28 TDX "C2'" "C2'" C 0 1 N N R -15.583 -2.864 65.548 -0.040 0.184 6.768 "C2'" TDX 29 TDX "O2'" "O2'" O 0 1 N N N -15.087 -4.055 66.149 -1.149 1.086 6.761 "O2'" TDX 30 TDX "C3'" "C3'" C 0 1 N N S -14.453 -1.824 65.540 1.264 0.978 6.879 "C3'" TDX 31 TDX "O3'" "O3'" O 0 1 N N N -13.326 -2.256 64.740 1.333 1.617 8.155 "O3'" TDX 32 TDX "C4'" "C4'" C 0 1 N N R -14.979 -0.500 64.998 2.441 0.008 6.725 "C4'" TDX 33 TDX "O4'" "O4'" O 0 1 N N N -13.982 0.520 65.058 3.666 0.742 6.678 "O4'" TDX 34 TDX H3 H3 H 0 1 N N N -22.616 -10.123 73.418 1.728 -2.360 -6.185 H3 TDX 35 TDX H5M1 1H5M H 0 0 N N N -19.278 -10.434 69.990 4.080 0.885 -8.329 H5M1 TDX 36 TDX H5M2 2H5M H 0 0 N N N -18.152 -9.039 70.211 2.797 2.076 -8.652 H5M2 TDX 37 TDX H5M3 3H5M H 0 0 N N N -18.263 -10.404 71.390 3.844 2.261 -7.225 H5M3 TDX 38 TDX H6 H6 H 0 1 N N N -19.587 -7.113 71.107 1.238 2.392 -6.440 H6 TDX 39 TDX H1B H1* H 0 1 N N N -22.136 -5.788 73.372 -0.564 2.286 -5.089 H1B TDX 40 TDX "H2'1" 1H2* H 0 0 N N N -19.256 -5.523 72.556 -2.565 1.460 -5.848 "H2'1" TDX 41 TDX "H2'2" 2H2* H 0 0 N N N -20.023 -4.903 73.875 -1.798 -0.124 -6.176 "H2'2" TDX 42 TDX H3B H3* H 0 1 N N N -19.640 -3.261 71.719 -2.457 -1.002 -4.100 H3B TDX 43 TDX "HO3'" *HO3 H 0 0 N N N -21.598 -2.046 72.270 -4.410 -0.035 -4.911 "HO3'" TDX 44 TDX H4B H4* H 0 1 N N N -22.236 -3.564 70.556 -2.284 1.809 -2.877 H4B TDX 45 TDX "H5'1" 1H5* H 0 0 N N N -20.331 -3.483 69.087 -2.944 -0.139 -1.431 "H5'1" TDX 46 TDX "H5'2" 2H5* H 0 0 N N N -21.138 -4.910 68.720 -1.437 -0.964 -1.896 "H5'2" TDX 47 TDX H2A H2A H 0 1 N N N -16.317 -6.006 69.044 -3.203 0.473 1.185 H2A TDX 48 TDX H2B H2B H 0 1 N N N -18.295 -0.839 69.270 -2.557 0.258 3.662 H2B TDX 49 TDX "H1'" "H1'" H 0 1 N N N -17.603 -3.094 66.268 -0.964 -1.168 5.370 "H1'" TDX 50 TDX H5B "1H5'" H 0 1 N N N -15.901 0.173 66.875 3.114 -1.459 5.299 H5B TDX 51 TDX H5D "2H5'" H 0 1 N N N -16.569 0.923 65.522 2.226 -0.093 4.585 H5D TDX 52 TDX "H2'" "H2'" H 0 1 N N N -15.915 -3.073 64.504 -0.128 -0.494 7.616 "H2'" TDX 53 TDX "HO2'" "'HO2" H 0 0 N N N -14.337 -4.383 65.667 -1.948 0.546 6.690 "HO2'" TDX 54 TDX "H3'" "H3'" H 0 1 N N N -14.101 -1.700 66.591 1.304 1.729 6.091 "H3'" TDX 55 TDX HO3A "'HO3" H 0 0 N N N -12.627 -1.613 64.735 2.175 2.092 8.184 HO3A TDX 56 TDX "H4'" "H4'" H 0 1 N N N -15.265 -0.642 63.930 2.461 -0.678 7.572 "H4'" TDX 57 TDX "HO4'" "'HO4" H 0 0 N N N -13.231 0.255 64.540 4.376 0.095 6.574 "HO4'" TDX 58 # 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 TDX O4 C4 DOUB N N 1 TDX C4 N3 SING N N 2 TDX C4 C5 SING N N 3 TDX N3 C2 SING N N 4 TDX N3 H3 SING N N 5 TDX C2 O2 DOUB N N 6 TDX C2 N1 SING N N 7 TDX C5 C5M SING N N 8 TDX C5 C6 DOUB N N 9 TDX C5M H5M1 SING N N 10 TDX C5M H5M2 SING N N 11 TDX C5M H5M3 SING N N 12 TDX C6 N1 SING N N 13 TDX C6 H6 SING N N 14 TDX N1 C1B SING N N 15 TDX C1B C2B SING N N 16 TDX C1B O4B SING N N 17 TDX C1B H1B SING N N 18 TDX C2B C3B SING N N 19 TDX C2B "H2'1" SING N N 20 TDX C2B "H2'2" SING N N 21 TDX C3B O3B SING N N 22 TDX C3B C4B SING N N 23 TDX C3B H3B SING N N 24 TDX O3B "HO3'" SING N N 25 TDX O4B C4B SING N N 26 TDX C4B C5B SING N N 27 TDX C4B H4B SING N N 28 TDX C5B O5B SING N N 29 TDX C5B "H5'1" SING N N 30 TDX C5B "H5'2" SING N N 31 TDX O5B PA SING N N 32 TDX PA O1A DOUB N N 33 TDX PA O2A SING N N 34 TDX PA O3A SING N N 35 TDX O2A H2A SING N N 36 TDX O3A PB SING N N 37 TDX PB O1B DOUB N N 38 TDX PB O2B SING N N 39 TDX PB "O1'" SING N N 40 TDX O2B H2B SING N N 41 TDX "O1'" "C1'" SING N N 42 TDX "C1'" "O5'" SING N N 43 TDX "C1'" "C2'" SING N N 44 TDX "C1'" "H1'" SING N N 45 TDX "O5'" "C5'" SING N N 46 TDX "C5'" "C4'" SING N N 47 TDX "C5'" H5B SING N N 48 TDX "C5'" H5D SING N N 49 TDX "C2'" "O2'" SING N N 50 TDX "C2'" "C3'" SING N N 51 TDX "C2'" "H2'" SING N N 52 TDX "O2'" "HO2'" SING N N 53 TDX "C3'" "O3'" SING N N 54 TDX "C3'" "C4'" SING N N 55 TDX "C3'" "H3'" SING N N 56 TDX "O3'" HO3A SING N N 57 TDX "C4'" "O4'" SING N N 58 TDX "C4'" "H4'" SING N N 59 TDX "O4'" "HO4'" SING N N 60 # 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 TDX SMILES ACDLabs 10.04 "O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O" TDX SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O" TDX SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O" TDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O" TDX SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(CO3)O)O)O)O" TDX InChI InChI 1.03 "InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1" TDX InChIKey InChI 1.03 AJUADKZRQSBUAK-KDGZBOQCSA-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 TDX "SYSTEMATIC NAME" ACDLabs 10.04 "[(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)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" TDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-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 TDX "Create component" 2001-11-23 PDBJ TDX "Modify descriptor" 2011-06-04 RCSB #