data_TRH # _chem_comp.id TRH _chem_comp.name "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 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 2000-11-28 _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 548.330 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TRH _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 1G3L _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 TRH O4P O4P O 0 1 N N N 14.715 62.773 52.230 0.500 1.102 -2.566 O4P TRH 1 TRH P2 P2 P 0 1 N N S 15.585 61.713 53.006 -0.506 -0.139 -2.753 P2 TRH 2 TRH O3P O3P O 0 1 N N N 16.478 60.604 52.238 -1.839 0.361 -3.155 O3P TRH 3 TRH O1 O1 O 0 1 N N N 16.412 62.544 54.070 0.063 -1.124 -3.892 O1 TRH 4 TRH C1 C1 C 0 1 N N R 17.700 62.115 54.383 0.151 -0.358 -5.095 C1 TRH 5 TRH C2 C2 C 0 1 N N R 17.672 61.865 55.846 -0.061 -1.277 -6.300 C2 TRH 6 TRH O2 O2 O 0 1 N N N 16.989 62.991 56.379 0.961 -2.275 -6.326 O2 TRH 7 TRH C3 C3 C 0 1 N N R 19.102 61.771 56.403 0.002 -0.442 -7.583 C3 TRH 8 TRH O3 O3 O 0 1 N N N 19.098 61.829 57.821 -0.046 -1.306 -8.720 O3 TRH 9 TRH C4 C4 C 0 1 N N R 19.938 62.867 55.797 1.315 0.347 -7.588 C4 TRH 10 TRH O4 O4 O 0 1 N N N 21.258 62.474 56.124 1.330 1.244 -8.701 O4 TRH 11 TRH C5 C5 C 0 1 N N S 19.623 62.900 54.277 1.423 1.145 -6.287 C5 TRH 12 TRH O5 O5 O 0 1 N N N 18.251 63.358 54.057 1.437 0.253 -5.174 O5 TRH 13 TRH C6 C6 C 0 1 N N N 20.675 63.684 53.489 2.714 1.965 -6.298 C6 TRH 14 TRH OPP OPP O 0 1 N N N 14.621 60.856 53.950 -0.631 -0.942 -1.363 OPP TRH 15 TRH P P P 0 1 N N S 14.283 59.294 53.688 -1.203 0.097 -0.275 P TRH 16 TRH O1P O1P O 0 1 N N N 12.937 59.154 54.505 -2.642 0.638 -0.754 O1P TRH 17 TRH O2P O2P O 0 1 N N N 15.539 58.321 53.947 -0.267 1.235 -0.141 O2P TRH 18 TRH "O5'" "O5'" O 0 1 N N N 13.978 59.217 52.141 -1.354 -0.642 1.146 "O5'" TRH 19 TRH "C5'" "C5'" C 0 1 N N N 12.896 60.016 51.674 -1.863 0.326 2.064 "C5'" TRH 20 TRH "C4'" "C4'" C 0 1 N N R 11.959 59.134 50.855 -2.031 -0.315 3.443 "C4'" TRH 21 TRH "O4'" "O4'" O 0 1 N N N 12.933 58.403 50.168 -0.753 -0.729 3.970 "O4'" TRH 22 TRH "C3'" "C3'" C 0 1 N N S 11.254 57.974 51.475 -2.531 0.728 4.474 "C3'" TRH 23 TRH "O3'" "O3'" O 0 1 N N N 9.914 57.927 51.018 -3.956 0.827 4.459 "O3'" TRH 24 TRH "C2'" "C2'" C 0 1 N N N 11.980 56.747 50.926 -2.032 0.125 5.811 "C2'" TRH 25 TRH "C1'" "C1'" C 0 1 N N R 12.576 57.173 49.604 -0.901 -0.835 5.396 "C1'" TRH 26 TRH N11 N11 N 0 1 N N N 13.697 56.328 49.213 0.348 -0.453 6.057 N11 TRH 27 TRH C21 C21 C 0 1 N N N 13.518 55.498 48.159 0.865 0.771 5.847 C21 TRH 28 TRH O21 O21 O 0 1 N N N 12.337 55.398 47.567 0.286 1.549 5.115 O21 TRH 29 TRH N31 N31 N 0 1 N N N 14.514 54.743 47.743 2.010 1.150 6.445 N31 TRH 30 TRH C41 C41 C 0 1 N N N 15.702 54.823 48.330 2.665 0.299 7.261 C41 TRH 31 TRH O41 O41 O 0 1 N N N 16.686 54.068 47.883 3.703 0.639 7.798 O41 TRH 32 TRH C51 C51 C 0 1 N N N 15.917 55.673 49.381 2.135 -0.994 7.485 C51 TRH 33 TRH C5A C5A C 0 1 N N N 17.288 55.714 50.013 2.847 -1.964 8.392 C5A TRH 34 TRH C61 C61 C 0 1 N N N 14.875 56.446 49.831 0.982 -1.346 6.877 C61 TRH 35 TRH H4PO OH4P H 0 0 N N N 14.190 63.424 52.681 1.355 0.733 -2.305 H4PO TRH 36 TRH HC1 HC1 H 0 1 N N N 18.178 61.219 53.923 -0.617 0.414 -5.089 HC1 TRH 37 TRH HC2 HC2 H 0 1 N N N 17.172 60.904 56.110 -1.036 -1.757 -6.224 HC2 TRH 38 TRH HO2 HO2 H 0 1 N N N 16.971 62.831 57.315 0.889 -2.771 -5.499 HO2 TRH 39 TRH HC3 HC3 H 0 1 N N N 19.549 60.788 56.125 -0.841 0.248 -7.612 HC3 TRH 40 TRH HO3 HO3 H 0 1 N N N 19.981 61.770 58.165 -0.881 -1.790 -8.668 HO3 TRH 41 TRH HC4 HC4 H 0 1 N N N 19.754 63.904 56.161 2.156 -0.342 -7.665 HC4 TRH 42 TRH HO4 HO4 H 0 1 N N N 21.785 63.165 55.741 2.171 1.719 -8.666 HO4 TRH 43 TRH HC5 HC5 H 0 1 N N N 19.684 61.862 53.872 0.568 1.816 -6.202 HC5 TRH 44 TRH HC61 1HC6 H 0 0 N N N 20.448 63.707 52.397 2.791 2.535 -5.372 HC61 TRH 45 TRH HC62 2HC6 H 0 0 N N N 20.802 64.713 53.897 3.570 1.294 -6.383 HC62 TRH 46 TRH HC63 3HC6 H 0 0 N N N 21.700 63.290 53.680 2.703 2.649 -7.146 HC63 TRH 47 TRH H1PO OH1P H 0 0 N N N 12.738 58.237 54.351 -3.220 -0.133 -0.829 H1PO TRH 48 TRH "H5'1" "1H5'" H 0 0 N N N 12.369 60.547 52.500 -1.165 1.161 2.135 "H5'1" TRH 49 TRH "H5'2" "2H5'" H 0 0 N N N 13.240 60.913 51.109 -2.829 0.689 1.712 "H5'2" TRH 50 TRH "H4'C" "CH4'" H 0 0 N N N 11.179 59.805 50.426 -2.717 -1.160 3.390 "H4'C" TRH 51 TRH "H3'C" "CH3'" H 0 0 N N N 11.252 58.033 52.588 -2.073 1.701 4.291 "H3'C" TRH 52 TRH "H3'O" "OH3'" H 0 0 N N N 9.465 57.188 51.412 -4.203 1.420 5.181 "H3'O" TRH 53 TRH "H2'1" "1H2'" H 0 0 N N N 12.727 56.318 51.633 -2.836 -0.422 6.303 "H2'1" TRH 54 TRH "H2'2" "2H2'" H 0 0 N N N 11.331 55.842 50.851 -1.647 0.908 6.465 "H2'2" TRH 55 TRH "H1'C" "CH1'" H 0 0 N N N 11.985 57.156 48.658 -1.165 -1.857 5.666 "H1'C" TRH 56 TRH H31N NH31 H 0 0 N N N 14.365 54.097 46.967 2.367 2.038 6.286 H31N TRH 57 TRH HCA1 1HCA H 0 0 N N N 17.463 56.406 50.869 3.751 -1.498 8.784 HCA1 TRH 58 TRH HCA2 2HCA H 0 0 N N N 17.574 54.681 50.320 2.191 -2.239 9.218 HCA2 TRH 59 TRH HCA3 3HCA H 0 0 N N N 18.044 55.921 49.220 3.115 -2.858 7.828 HCA3 TRH 60 TRH H61C CH61 H 0 0 N N N 14.982 57.149 50.673 0.562 -2.328 7.036 H61C TRH 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 TRH O4P P2 SING N N 1 TRH O4P H4PO SING N N 2 TRH P2 O3P DOUB N N 3 TRH P2 O1 SING N N 4 TRH P2 OPP SING N N 5 TRH O1 C1 SING N N 6 TRH C1 C2 SING N N 7 TRH C1 O5 SING N N 8 TRH C1 HC1 SING N N 9 TRH C2 O2 SING N N 10 TRH C2 C3 SING N N 11 TRH C2 HC2 SING N N 12 TRH O2 HO2 SING N N 13 TRH C3 O3 SING N N 14 TRH C3 C4 SING N N 15 TRH C3 HC3 SING N N 16 TRH O3 HO3 SING N N 17 TRH C4 O4 SING N N 18 TRH C4 C5 SING N N 19 TRH C4 HC4 SING N N 20 TRH O4 HO4 SING N N 21 TRH C5 O5 SING N N 22 TRH C5 C6 SING N N 23 TRH C5 HC5 SING N N 24 TRH C6 HC61 SING N N 25 TRH C6 HC62 SING N N 26 TRH C6 HC63 SING N N 27 TRH OPP P SING N N 28 TRH P O1P SING N N 29 TRH P O2P DOUB N N 30 TRH P "O5'" SING N N 31 TRH O1P H1PO SING N N 32 TRH "O5'" "C5'" SING N N 33 TRH "C5'" "C4'" SING N N 34 TRH "C5'" "H5'1" SING N N 35 TRH "C5'" "H5'2" SING N N 36 TRH "C4'" "O4'" SING N N 37 TRH "C4'" "C3'" SING N N 38 TRH "C4'" "H4'C" SING N N 39 TRH "O4'" "C1'" SING N N 40 TRH "C3'" "O3'" SING N N 41 TRH "C3'" "C2'" SING N N 42 TRH "C3'" "H3'C" SING N N 43 TRH "O3'" "H3'O" SING N N 44 TRH "C2'" "C1'" SING N N 45 TRH "C2'" "H2'1" SING N N 46 TRH "C2'" "H2'2" SING N N 47 TRH "C1'" N11 SING N N 48 TRH "C1'" "H1'C" SING N N 49 TRH N11 C21 SING N N 50 TRH N11 C61 SING N N 51 TRH C21 O21 DOUB N N 52 TRH C21 N31 SING N N 53 TRH N31 C41 SING N N 54 TRH N31 H31N SING N N 55 TRH C41 O41 DOUB N N 56 TRH C41 C51 SING N N 57 TRH C51 C5A SING N N 58 TRH C51 C61 DOUB N N 59 TRH C5A HCA1 SING N N 60 TRH C5A HCA2 SING N N 61 TRH C5A HCA3 SING N N 62 TRH C61 H61C 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 TRH SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O" TRH 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](O)[C@H]1O" TRH 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](O)[CH]1O" TRH 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)O)O" TRH 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)O)O" TRH 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+/m0/s1" TRH InChIKey InChI 1.03 ZOSQFDVXNQFKBY-CGAXJHMRSA-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 TRH "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,4R,5R,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" TRH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] [(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-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 TRH "Create component" 2000-11-28 EBI TRH "Modify descriptor" 2011-06-04 RCSB #