data_TED # _chem_comp.id TED _chem_comp.name ;5-[(1E)-14-carboxy-10,13-bis(carboxymethyl)-3,8-dioxo-4,7,10,13-tetraazatetradec-1-en-1-yl]-2'-deoxyuridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C24 H35 N6 O16 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-22 _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 694.539 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TED _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 2KY8 _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 TED P P P 0 1 N N N -16.425 -9.972 37.354 -11.396 2.869 -0.735 P TED 1 TED N1 N1 N 0 1 N N N -14.567 -11.434 32.735 -6.245 -1.315 0.209 N1 TED 2 TED C2 C2 C 0 1 N N N -13.506 -11.560 31.861 -6.172 -0.689 1.394 C2 TED 3 TED O2 O2 O 0 1 N N N -13.476 -10.976 30.780 -7.201 -0.341 1.939 O2 TED 4 TED N3 N3 N 0 1 N N N -12.477 -12.383 32.274 -4.998 -0.433 1.996 N3 TED 5 TED C4 C4 C 0 1 N N N -12.420 -13.081 33.468 -3.836 -0.806 1.419 C4 TED 6 TED O4 O4 O 0 1 N N N -11.450 -13.787 33.734 -2.771 -0.577 1.961 O4 TED 7 TED C5 C5 C 0 1 N N N -13.573 -12.890 34.321 -3.887 -1.496 0.118 C5 TED 8 TED C6 C6 C 0 1 N N N -14.590 -12.090 33.936 -5.128 -1.727 -0.447 C6 TED 9 TED C7 C7 C 0 1 N N N -13.640 -13.594 35.652 -2.659 -1.924 -0.557 C7 TED 10 TED C8 C8 C 0 1 N N N -14.776 -14.160 36.049 -1.453 -1.618 -0.025 C8 TED 11 TED C9 C9 C 0 1 N N N -14.847 -14.827 37.358 -0.267 -1.931 -0.733 C9 TED 12 TED O9 O9 O 0 1 N N N -14.995 -16.032 37.420 -0.332 -2.476 -1.821 O9 TED 13 TED "C1'" "C1'" C 0 1 N N R -15.684 -10.563 32.324 -7.559 -1.567 -0.387 "C1'" TED 14 TED N10 N10 N 0 1 N N N -14.749 -14.101 38.490 0.935 -1.627 -0.204 N10 TED 15 TED C11 C11 C 0 1 N N N -14.831 -14.763 39.794 2.161 -1.951 -0.936 C11 TED 16 TED C12 C12 C 0 1 N N N -13.892 -15.971 39.813 3.376 -1.503 -0.120 C12 TED 17 TED N13 N13 N 0 1 N N N -13.280 -16.094 41.139 4.603 -1.827 -0.853 N13 TED 18 TED "C2'" "C2'" C 0 1 N N N -17.061 -11.199 32.533 -8.360 -2.540 0.499 "C2'" TED 19 TED "C3'" "C3'" C 0 1 N N S -17.850 -10.053 33.121 -9.641 -1.753 0.866 "C3'" TED 20 TED "O3'" "O3'" O 0 1 N N N -18.750 -9.530 32.141 -10.792 -2.600 0.815 "O3'" TED 21 TED "C4'" "C4'" C 0 1 N N R -16.933 -8.934 33.557 -9.694 -0.680 -0.251 "C4'" TED 22 TED "O4'" "O4'" O 0 1 N N N -15.630 -9.282 33.063 -8.307 -0.341 -0.458 "O4'" TED 23 TED "C5'" "C5'" C 0 1 N N N -16.869 -8.729 35.067 -10.485 0.544 0.215 "C5'" TED 24 TED "O5'" "O5'" O 0 1 N N N -16.565 -9.947 35.751 -10.618 1.466 -0.868 "O5'" TED 25 TED CY1 CY1 C 0 1 N N N -13.410 -16.517 43.576 7.066 -1.856 -1.076 CY1 TED 26 TED OY1 OY1 O 0 1 N N N -15.273 -16.533 42.075 5.869 -0.980 0.760 OY1 TED 27 TED CY2 CY2 C 0 1 N N N -17.023 -16.416 46.746 8.139 2.811 0.757 CY2 TED 28 TED OY2 OY2 O 0 1 N N N -16.594 -15.346 44.656 8.828 4.577 -0.643 OY2 TED 29 TED CY3 CY3 C 0 1 N N N -16.896 -18.769 46.723 10.546 2.748 1.010 CY3 TED 30 TED OY3 OY3 O 0 1 N N N -18.197 -18.674 44.725 11.745 1.856 -0.812 OY3 TED 31 TED CY4 CY4 C 0 1 N N N -14.031 -18.667 44.315 9.473 -1.919 -0.823 CY4 TED 32 TED OY4 OY4 O 0 1 N N N -15.543 -18.957 42.492 10.680 -4.048 -0.491 OY4 TED 33 TED CY5 CY5 C 0 1 N N N -14.045 -16.390 42.209 5.804 -1.522 -0.323 CY5 TED 34 TED CY6 CY6 C 0 1 N N N -16.799 -15.206 45.875 8.017 4.192 0.165 CY6 TED 35 TED OY6 OY6 O 0 1 N N N -16.819 -14.098 46.362 7.006 4.994 0.536 OY6 TED 36 TED CY7 CY7 C 0 1 N N N -18.124 -19.068 45.903 11.809 2.406 0.262 CY7 TED 37 TED OY7 OY7 O 0 1 N N N -19.040 -19.692 46.389 13.005 2.711 0.789 OY7 TED 38 TED CY8 CY8 C 0 1 N N N -14.380 -19.093 42.912 9.601 -3.295 -0.221 CY8 TED 39 TED OY8 OY8 O 0 1 N N N -13.529 -19.568 42.195 8.734 -3.721 0.504 OY8 TED 40 TED CYA CYA C 0 1 N N N -13.927 -16.879 45.847 8.277 0.162 -0.507 CYA TED 41 TED NYA NYA N 0 1 N N N -14.320 -17.236 44.477 8.223 -1.299 -0.363 NYA TED 42 TED CYB CYB C 0 1 N N N -14.924 -17.484 46.838 9.335 0.730 0.441 CYB TED 43 TED NYB NYB N 0 1 N N N -16.254 -17.549 46.216 9.389 2.191 0.297 NYB TED 44 TED OP3 O3P O 0 1 N Y N -16.384 -11.375 37.824 -12.957 2.594 -0.454 O3P TED 45 TED OP1 O1P O 0 1 N N N -14.975 -9.170 37.815 -10.822 3.647 0.387 O1P TED 46 TED OP2 O2P O 0 1 N N N -17.773 -9.170 38.060 -11.236 3.704 -2.103 O2P TED 47 TED HN3 HN3 H 0 1 N N N -11.700 -12.484 31.652 -4.985 0.023 2.853 HN3 TED 48 TED H6 H6 H 0 1 N N N -15.440 -11.965 34.590 -5.209 -2.230 -1.400 H6 TED 49 TED H7 H7 H 0 1 N N N -12.765 -13.639 36.284 -2.716 -2.484 -1.479 H7 TED 50 TED H8 H8 H 0 1 N N N -15.646 -14.130 35.410 -1.394 -1.135 0.939 H8 TED 51 TED "H1'" "H1'" H 0 1 N N N -15.559 -10.397 31.244 -7.439 -1.988 -1.386 "H1'" TED 52 TED HN10 HN10 H 0 0 N N N -14.620 -13.111 38.439 0.987 -1.193 0.662 HN10 TED 53 TED H11 H11 H 0 1 N N N -14.535 -14.056 40.583 2.212 -3.027 -1.102 H11 TED 54 TED H11A H11A H 0 0 N N N -15.864 -15.099 39.971 2.159 -1.435 -1.896 H11A TED 55 TED H12 H12 H 0 1 N N N -14.464 -16.883 39.587 3.325 -0.427 0.045 H12 TED 56 TED H12A H12A H 0 0 N N N -13.105 -15.835 39.057 3.379 -2.019 0.840 H12A TED 57 TED HN13 HN13 H 0 0 N N N -12.295 -15.958 41.250 4.550 -2.261 -1.719 HN13 TED 58 TED "H2'" "H2'" H 0 1 N N N -17.497 -11.559 31.589 -8.612 -3.443 -0.057 "H2'" TED 59 TED "H2'A" "H2'A" H 0 0 N N N -17.018 -12.063 33.213 -7.795 -2.790 1.397 "H2'A" TED 60 TED "H3'" "H3'" H 0 1 N N N -18.403 -10.438 33.991 -9.545 -1.289 1.847 "H3'" TED 61 TED "HO3'" "HO3'" H 0 0 N N N -19.243 -8.810 32.516 -10.762 -3.341 1.435 "HO3'" TED 62 TED "H4'" "H4'" H 0 1 N N N -17.316 -7.984 33.157 -10.131 -1.094 -1.160 "H4'" TED 63 TED "H5'" "H5'" H 0 1 N N N -16.084 -7.992 35.291 -11.474 0.232 0.550 "H5'" TED 64 TED "H5'A" "H5'A" H 0 0 N N N -17.845 -8.361 35.416 -9.958 1.025 1.039 "H5'A" TED 65 TED HY1 HY1 H 0 1 N N N -13.211 -15.514 43.981 7.170 -2.938 -1.149 HY1 TED 66 TED HY1A HY1A H 0 0 N N N -12.465 -17.073 43.490 7.015 -1.428 -2.077 HY1A TED 67 TED HY2 HY2 H 0 1 N N N -16.692 -16.196 47.772 8.147 2.881 1.844 HY2 TED 68 TED HY2A HY2A H 0 0 N N N -18.093 -16.670 46.753 7.293 2.203 0.438 HY2A TED 69 TED HY3 HY3 H 0 1 N N N -17.184 -18.622 47.774 10.593 2.325 2.014 HY3 TED 70 TED HY3A HY3A H 0 0 N N N -16.192 -19.611 46.650 10.445 3.831 1.076 HY3A TED 71 TED HY4 HY4 H 0 1 N N N -12.962 -18.848 44.498 10.319 -1.306 -0.511 HY4 TED 72 TED HY4A HY4A H 0 0 N N N -14.629 -19.246 45.034 9.462 -1.997 -1.910 HY4A TED 73 TED HOY4 HOY4 H 0 0 N Y N -15.596 -19.272 41.597 10.718 -4.923 -0.083 HOY4 TED 74 TED HOY6 HOY6 H 0 0 N Y N -16.662 -13.451 45.684 6.969 5.870 0.130 HOY6 TED 75 TED HOY7 HOY7 H 0 0 N Y N -19.731 -19.794 45.745 13.787 2.472 0.273 HOY7 TED 76 TED HYA HYA H 0 1 N N N -13.923 -15.784 45.954 8.536 0.417 -1.535 HYA TED 77 TED HYAA HYAA H 0 0 N N N -12.920 -17.272 46.054 7.304 0.588 -0.262 HYAA TED 78 TED HYB HYB H 0 1 N N N -14.598 -18.498 47.114 9.076 0.475 1.469 HYB TED 79 TED HYBA HYBA H 0 0 N N N -14.971 -16.856 47.740 10.308 0.304 0.196 HYBA TED 80 TED HOP3 HO3P H 0 0 N Y N -15.566 -11.533 38.280 -13.398 2.088 -1.149 HO3P TED 81 TED HOP2 HO2P H 0 0 N N N -17.469 -8.432 38.575 -11.680 4.562 -2.094 HO2P TED 82 # 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 TED N1 C6 SING N N 1 TED C2 N1 SING N N 2 TED C2 N3 SING N N 3 TED O2 C2 DOUB N N 4 TED N3 C4 SING N N 5 TED C4 O4 DOUB N N 6 TED C4 C5 SING N N 7 TED C5 C7 SING N N 8 TED C6 C5 DOUB N N 9 TED C7 C8 DOUB N N 10 TED C8 C9 SING N N 11 TED C9 O9 DOUB N N 12 TED C9 N10 SING N N 13 TED "C1'" N1 SING N N 14 TED "C1'" "C2'" SING N E 15 TED "C1'" "O4'" SING N N 16 TED N10 C11 SING N N 17 TED C11 C12 SING N N 18 TED C12 N13 SING N N 19 TED N13 CY5 SING N N 20 TED "C2'" "C3'" SING N N 21 TED "C3'" "C4'" SING N N 22 TED "O3'" "C3'" SING N N 23 TED "C4'" "C5'" SING N N 24 TED "O4'" "C4'" SING N N 25 TED "C5'" "O5'" SING N N 26 TED "O5'" P SING N N 27 TED CY1 NYA SING N N 28 TED OY1 CY5 DOUB N N 29 TED OY2 CY6 DOUB N N 30 TED OY3 CY7 DOUB N N 31 TED CY4 NYA SING N N 32 TED OY4 CY8 SING N N 33 TED CY5 CY1 SING N N 34 TED CY6 CY2 SING N N 35 TED CY6 OY6 SING N N 36 TED CY7 CY3 SING N N 37 TED CY7 OY7 SING N N 38 TED CY8 CY4 SING N N 39 TED OY8 CY8 DOUB N N 40 TED CYA CYB SING N N 41 TED NYA CYA SING N N 42 TED NYB CY2 SING N N 43 TED NYB CY3 SING N N 44 TED NYB CYB SING N N 45 TED P OP3 SING N N 46 TED P OP1 DOUB N N 47 TED P OP2 SING N N 48 TED N3 HN3 SING N N 49 TED C6 H6 SING N N 50 TED C7 H7 SING N N 51 TED C8 H8 SING N N 52 TED "C1'" "H1'" SING N N 53 TED N10 HN10 SING N N 54 TED C11 H11 SING N N 55 TED C11 H11A SING N N 56 TED C12 H12 SING N N 57 TED C12 H12A SING N N 58 TED N13 HN13 SING N N 59 TED "C2'" "H2'" SING N N 60 TED "C2'" "H2'A" SING N N 61 TED "C3'" "H3'" SING N N 62 TED "O3'" "HO3'" SING N N 63 TED "C4'" "H4'" SING N N 64 TED "C5'" "H5'" SING N N 65 TED "C5'" "H5'A" SING N N 66 TED CY1 HY1 SING N N 67 TED CY1 HY1A SING N N 68 TED CY2 HY2 SING N N 69 TED CY2 HY2A SING N N 70 TED CY3 HY3 SING N N 71 TED CY3 HY3A SING N N 72 TED CY4 HY4 SING N N 73 TED CY4 HY4A SING N N 74 TED OY4 HOY4 SING N N 75 TED OY6 HOY6 SING N N 76 TED OY7 HOY7 SING N N 77 TED CYA HYA SING N N 78 TED CYA HYAA SING N N 79 TED CYB HYB SING N N 80 TED CYB HYBA SING N N 81 TED OP3 HOP3 SING N N 82 TED OP2 HOP2 SING N N 83 # 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 TED SMILES ACDLabs 12.01 "O=C(O)CN(CC(=O)O)CCN(CC(=O)O)CC(=O)NCCNC(=O)\C=C\C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O" TED SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(\C=C\C(=O)NCCNC(=O)CN(CCN(CC(O)=O)CC(O)=O)CC(O)=O)C(=O)NC2=O" TED SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=CC(=O)NCCNC(=O)CN(CCN(CC(O)=O)CC(O)=O)CC(O)=O)C(=O)NC2=O" TED SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)/C=C/C(=O)NCCNC(=O)C[N@](CCN(CC(=O)O)CC(=O)O)CC(=O)O)COP(=O)(O)O)O" TED SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)C=CC(=O)NCCNC(=O)CN(CCN(CC(=O)O)CC(=O)O)CC(=O)O)COP(=O)(O)O)O" TED InChI InChI 1.03 ;InChI=1S/C24H35N6O16P/c31-15-7-19(46-16(15)13-45-47(42,43)44)30-8-14(23(40)27-24(30)41)1-2-17(32)25-3-4-26-18(33)9-28(10-20(34)35)5-6-29(11-21(36)37)12-22(38)39/h1-2,8,15-16,19,31H,3-7,9-13H2,(H,25,32)(H,26,33)(H,34,35)(H,36,37)(H,38,39)(H,27,40,41)(H2,42,43,44)/b2-1+/t15-,16+,19+/m0/s1 ; TED InChIKey InChI 1.03 GANOOALIPBDIPI-DARGZDBCSA-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 TED "SYSTEMATIC NAME" ACDLabs 12.01 ;5-[(13E)-1-carboxy-2,5-bis(carboxymethyl)-7,12-dioxo-2,5,8,11-tetraazatetradec-13-en-14-yl]-2'-deoxyuridine 5'-(dihydrogen phosphate) ; TED "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "2-[carboxymethyl-[2-[carboxymethyl-[2-[2-[[(E)-3-[1-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-dioxo-pyrimidin-5-yl]prop-2-enoyl]amino]ethylamino]-2-oxo-ethyl]amino]ethyl]amino]ethanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TED "Create component" 2010-07-22 RCSB TED "Modify descriptor" 2011-06-04 RCSB #