data_TTD # _chem_comp.id TTD _chem_comp.name "CIS-SYN CYCLOBUTANE THYMINE DIMER" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C20 H28 N4 O15 P2" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ;[(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-DIHYDROXY-15A,15B-DIMETHYL-7-OXIDO-13,15,16,18-TETRAOXOHEXADECAHYDRO-1H-1,4-EPOX Y-9,12-METHANO-6,8,11-TRIOXA-12A,14,17,18A-TETRAAZA-7-PHOSPHACYCLOHEXADECA[1,2,3,4-DEF]BIPHENYLEN-10-YL]METHYL DIHYDROGEN PHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-03-16 _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 626.402 _chem_comp.one_letter_code T _chem_comp.three_letter_code TTD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1SKS _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 TTD P P P 0 1 N N N 44.974 34.117 22.754 3.395 -5.992 1.952 P TTD 1 TTD OP1 O1P O 0 1 N N N 44.423 33.598 24.035 4.834 -6.355 2.179 OP1 TTD 2 TTD OP2 O2P O 0 1 N N N 46.404 33.880 22.420 2.701 -6.689 0.668 OP2 TTD 3 TTD OP3 O3P O 0 1 N Y N ? ? ? 2.396 -6.370 3.166 OP3 TTD 4 TTD "O5'" O5* O 0 1 N N N 44.083 33.560 21.554 3.115 -4.413 1.730 "O5'" TTD 5 TTD "C5'" C5* C 0 1 N N N 43.721 32.176 21.480 1.782 -3.987 1.509 "C5'" TTD 6 TTD C4R C4R C 0 1 N N R 42.875 31.901 20.214 1.777 -2.481 1.332 C4R TTD 7 TTD "O4'" O4* O 0 1 N N N 41.463 32.019 20.410 2.556 -2.111 0.176 "O4'" TTD 8 TTD C3R C3R C 0 1 N N S 43.340 32.850 19.086 0.401 -1.890 1.074 C3R TTD 9 TTD O3R O3R O 0 1 N N N 44.013 31.900 18.151 -0.367 -1.741 2.249 O3R TTD 10 TTD "C2'" C2* C 0 1 N N N 41.939 33.463 18.719 0.798 -0.553 0.489 "C2'" TTD 11 TTD "C1'" C1* C 0 1 N N R 40.983 32.313 19.088 1.946 -0.942 -0.423 "C1'" TTD 12 TTD N1 N1 N 0 1 N N N 39.492 32.476 19.390 1.549 -1.214 -1.824 N1 TTD 13 TTD C2 C2 C 0 1 N N N 38.939 31.199 19.708 1.866 -0.236 -2.782 C2 TTD 14 TTD O2 O2 O 0 1 N N N 39.604 30.166 19.707 2.082 0.948 -2.511 O2 TTD 15 TTD N3 N3 N 0 1 N N N 37.649 31.143 20.023 2.025 -0.707 -4.091 N3 TTD 16 TTD C4 C4 C 0 1 N N N 36.762 32.177 20.092 2.113 -2.028 -4.537 C4 TTD 17 TTD O4 O4 O 0 1 N N N 35.610 31.912 20.413 2.529 -2.299 -5.668 O4 TTD 18 TTD C5 C5 C 0 1 N N R 37.282 33.546 19.775 1.668 -3.089 -3.502 C5 TTD 19 TTD C5A C5A C 0 1 N N N 37.112 34.198 21.243 2.833 -3.997 -3.153 C5A TTD 20 TTD C6 C6 C 0 1 N N R 38.653 33.664 19.399 1.048 -2.561 -2.201 C6 TTD 21 TTD PB PB P 0 1 N N S 44.894 32.047 16.774 -1.850 -2.393 2.325 PB TTD 22 TTD O5P O5P O 0 1 N N N 45.040 33.260 15.971 -2.634 -1.999 3.544 O5P TTD 23 TTD O4P O4P O 0 1 N N N 45.126 30.599 16.363 -1.573 -3.983 2.202 O4P TTD 24 TTD O5R O5R O 0 1 N N N 43.554 31.920 15.856 -2.545 -2.031 0.908 O5R TTD 25 TTD C5R C5R C 0 1 N N N 42.675 33.043 15.611 -2.889 -0.679 0.642 C5R TTD 26 TTD O4R O4R O 0 1 N N N 40.473 32.845 16.394 -1.663 -0.657 -1.483 O4R TTD 27 TTD C2R C2R C 0 1 N N N 39.646 34.260 14.801 -3.400 -1.041 -3.061 C2R TTD 28 TTD C1R C1R C 0 1 N N R 39.305 33.194 15.800 -1.904 -0.717 -2.898 C1R TTD 29 TTD N1T N1T N 0 1 N N N 38.182 33.620 16.723 -1.043 -1.680 -3.599 N1T TTD 30 TTD C2T C2T C 0 1 N N N 36.952 33.215 16.205 -1.164 -1.661 -5.007 C2T TTD 31 TTD O2T O2T O 0 1 N N N 36.816 32.602 15.165 -1.664 -0.721 -5.636 O2T TTD 32 TTD N3T N3T N 0 1 N N N 35.847 33.524 16.901 -0.761 -2.811 -5.687 N3T TTD 33 TTD C4T C4T C 0 1 N N N 35.800 34.214 18.093 -0.153 -3.956 -5.191 C4T TTD 34 TTD O4T O4T O 0 1 N N N 34.661 34.368 18.522 0.006 -4.965 -5.883 O4T TTD 35 TTD C5T C5T C 0 1 N N S 37.128 34.660 18.665 0.314 -3.831 -3.741 C5T TTD 36 TTD C5M C5M C 0 1 N N N 36.886 36.124 19.248 0.269 -5.202 -3.079 C5M TTD 37 TTD C6T C6T C 0 1 N N S 38.226 34.362 18.002 -0.367 -2.772 -2.831 C6T TTD 38 TTD "C4'" C4* C 0 1 N N R 41.270 32.603 15.259 -2.936 -0.421 -0.857 "C4'" TTD 39 TTD "C3'" C3* C 0 1 N N S 40.770 33.511 14.140 -3.871 -1.311 -1.646 "C3'" TTD 40 TTD "O3'" O3* O 0 1 N N N 40.328 32.738 13.021 -5.222 -0.953 -1.453 "O3'" TTD 41 TTD HOP2 2HOP H 0 0 N N N 46.755 34.211 21.602 2.798 -7.657 0.543 HOP2 TTD 42 TTD HOP3 3HOP H 0 0 N N N 0.351 0.331 -0.817 2.441 -7.269 3.556 HOP3 TTD 43 TTD "H5'" 1H5* H 0 1 N N N 44.614 31.511 21.533 1.395 -4.472 0.612 "H5'" TTD 44 TTD "H5''" 2H5* H 0 0 N N N 43.203 31.833 22.406 1.170 -4.266 2.368 "H5''" TTD 45 TTD H4R H4R H 0 1 N N N 43.045 30.834 19.938 2.242 -2.028 2.215 H4R TTD 46 TTD H3R H3R H 0 1 N N N 44.062 33.689 19.212 -0.139 -2.484 0.330 H3R TTD 47 TTD "H2'" 1H2* H 0 1 N N N 41.709 34.441 19.201 0.000 0.000 -0.000 "H2'" TTD 48 TTD "H2''" 2H2* H 0 0 N N N 41.846 33.838 17.673 1.161 0.098 1.296 "H2''" TTD 49 TTD "H1'" H1* H 0 1 N N N 41.003 31.650 18.191 2.703 -0.151 -0.423 "H1'" TTD 50 TTD HN3 HN3 H 0 1 N N N 37.302 30.207 20.234 2.264 0.001 -4.781 HN3 TTD 51 TTD H5A1 1H5A H 0 0 N N N 37.499 35.216 21.007 3.454 -4.177 -4.036 H5A1 TTD 52 TTD H5A2 2H5A H 0 0 N N N 36.096 34.142 21.700 3.459 -3.547 -2.377 H5A2 TTD 53 TTD H5A3 3H5A H 0 0 N N N 37.601 33.660 22.088 2.469 -4.962 -2.786 H5A3 TTD 54 TTD H6 H6 H 0 1 N N N 39.373 34.184 20.072 1.221 -3.289 -1.398 H6 TTD 55 TTD H4P H4P H 0 1 N N N 45.635 30.684 15.566 -2.334 -4.600 2.253 H4P TTD 56 TTD H5R1 1H5R H 0 0 N N N 42.672 33.749 16.474 -2.149 -0.021 1.108 H5R1 TTD 57 TTD H5R2 2H5R H 0 0 N N N 43.093 33.719 14.829 -3.863 -0.478 1.099 H5R2 TTD 58 TTD H2R1 1H2R H 0 0 N N N 38.823 34.631 14.146 -3.605 -1.891 -3.719 H2R1 TTD 59 TTD H2R2 2H2R H 0 0 N N N 39.870 35.278 15.194 -3.926 -0.180 -3.492 H2R2 TTD 60 TTD H1R H1R H 0 1 N N N 38.873 32.281 15.326 -1.695 0.277 -3.313 H1R TTD 61 TTD HT HT H 0 1 N N N 34.969 33.207 16.489 -0.969 -2.822 -6.682 HT TTD 62 TTD H71 1H5M H 0 1 N N N 36.777 36.910 18.464 0.847 -5.930 -3.657 H71 TTD 63 TTD H72 2H5M H 0 1 N N N 36.008 36.132 19.935 0.684 -5.158 -2.068 H72 TTD 64 TTD H73 3H5M H 0 1 N N N 37.691 36.397 19.968 -0.764 -5.557 -3.013 H73 TTD 65 TTD H6T H6T H 0 1 N N N 38.860 35.109 17.471 -1.078 -3.228 -2.130 H6T TTD 66 TTD "H4'" H4* H 0 1 N N N 41.235 31.532 14.950 -3.196 0.637 -1.002 "H4'" TTD 67 TTD H1 H1 H 0 1 N N N 41.548 34.192 13.722 -3.736 -2.371 -1.403 H1 TTD 68 TTD "HO3'" H3T H 0 0 N Y N 41.038 32.264 12.603 -5.700 -1.244 -2.244 "HO3'" TTD 69 # # 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 TTD P OP1 DOUB N N 1 TTD P OP2 SING N N 2 TTD P OP3 SING N N 3 TTD P "O5'" SING N N 4 TTD OP2 HOP2 SING N N 5 TTD OP3 HOP3 SING N N 6 TTD "O5'" "C5'" SING N N 7 TTD "C5'" C4R SING N N 8 TTD "C5'" "H5'" SING N N 9 TTD "C5'" "H5''" SING N N 10 TTD C4R "O4'" SING N N 11 TTD C4R C3R SING N N 12 TTD C4R H4R SING N N 13 TTD "O4'" "C1'" SING N N 14 TTD C3R O3R SING N N 15 TTD C3R "C2'" SING N N 16 TTD C3R H3R SING N N 17 TTD O3R PB SING N N 18 TTD "C2'" "C1'" SING N N 19 TTD "C2'" "H2'" SING N N 20 TTD "C2'" "H2''" SING N N 21 TTD "C1'" N1 SING N N 22 TTD "C1'" "H1'" SING N N 23 TTD N1 C2 SING N N 24 TTD N1 C6 SING N N 25 TTD C2 O2 DOUB N N 26 TTD C2 N3 SING N N 27 TTD N3 C4 SING N N 28 TTD N3 HN3 SING N N 29 TTD C4 O4 DOUB N N 30 TTD C4 C5 SING N N 31 TTD C5 C5A SING N N 32 TTD C5 C6 SING N N 33 TTD C5 C5T SING N N 34 TTD C5A H5A1 SING N N 35 TTD C5A H5A2 SING N N 36 TTD C5A H5A3 SING N N 37 TTD C6 C6T SING N N 38 TTD C6 H6 SING N N 39 TTD PB O5P DOUB N N 40 TTD PB O4P SING N N 41 TTD PB O5R SING N N 42 TTD O4P H4P SING N N 43 TTD O5R C5R SING N N 44 TTD C5R "C4'" SING N N 45 TTD C5R H5R1 SING N N 46 TTD C5R H5R2 SING N N 47 TTD O4R C1R SING N N 48 TTD O4R "C4'" SING N N 49 TTD C2R C1R SING N N 50 TTD C2R "C3'" SING N N 51 TTD C2R H2R1 SING N N 52 TTD C2R H2R2 SING N N 53 TTD C1R N1T SING N N 54 TTD C1R H1R SING N N 55 TTD N1T C2T SING N N 56 TTD N1T C6T SING N N 57 TTD C2T O2T DOUB N N 58 TTD C2T N3T SING N N 59 TTD N3T C4T SING N N 60 TTD N3T HT SING N N 61 TTD C4T O4T DOUB N N 62 TTD C4T C5T SING N N 63 TTD C5T C5M SING N N 64 TTD C5T C6T SING N N 65 TTD C5M H71 SING N N 66 TTD C5M H72 SING N N 67 TTD C5M H73 SING N N 68 TTD C6T H6T SING N N 69 TTD "C4'" "C3'" SING N N 70 TTD "C4'" "H4'" SING N N 71 TTD "C3'" "O3'" SING N N 72 TTD "C3'" H1 SING N N 73 TTD "O3'" "HO3'" SING N N 74 # # 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 TTD SMILES ACDLabs 10.04 "O=C1NC(=O)C5(C4N1C2OC(C(O)C2)COP(=O)(O)OC6C(OC(N3C(=O)NC(=O)C5(C34)C)C6)COP(=O)(O)O)C" TTD SMILES_CANONICAL CACTVS 3.341 "C[C@]12[C@H]3[C@@H]4N([C@H]5C[C@H](O[P@](O)(=O)OC[C@H]6O[C@H](C[C@@H]6O)N3C(=O)NC1=O)[C@@H](CO[P](O)(O)=O)O5)C(=O)NC(=O)[C@]24C" TTD SMILES CACTVS 3.341 "C[C]12[CH]3[CH]4N([CH]5C[CH](O[P](O)(=O)OC[CH]6O[CH](C[CH]6O)N3C(=O)NC1=O)[CH](CO[P](O)(O)=O)O5)C(=O)NC(=O)[C]24C" TTD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@]12[C@H]3[C@H]4[C@@]1(C(=O)NC(=O)N4[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O[P@@](=O)(OC[C@@H]6[C@H](C[C@H](N3C(=O)NC2=O)O6)O)O)C" TTD SMILES "OpenEye OEToolkits" 1.5.0 "CC12C3C4C1(C(=O)NC(=O)N4C5CC(C(O5)COP(=O)(O)O)OP(=O)(OCC6C(CC(N3C(=O)NC2=O)O6)O)O)C" TTD InChI InChI 1.03 "InChI=1S/C20H28N4O15P2/c1-19-13-14-20(19,2)16(27)22-18(29)24(14)12-4-8(10(38-12)6-35-40(30,31)32)39-41(33,34)36-5-9-7(25)3-11(37-9)23(13)17(28)21-15(19)26/h7-14,25H,3-6H2,1-2H3,(H,33,34)(H,21,26,28)(H,22,27,29)(H2,30,31,32)/t7-,8-,9+,10+,11+,12+,13+,14-,19-,20+/m0/s1" TTD InChIKey InChI 1.03 LWAHHJJPLXBMFO-MQBJNLFFSA-N # _pdbx_chem_comp_identifier.comp_id TTD _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 10.04 _pdbx_chem_comp_identifier.identifier "[(1R,3R,4S,6S,9R,10S,12R,15aS,15bR,18bR,18cS)-6,10-dihydroxy-15a,15b-dimethyl-6-oxido-13,15,16,18-tetraoxohexadecahydro-8H-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraaza-6-phosphacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl dihydrogen 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 TTD "Create component" 2004-03-16 PDBJ TTD "Modify descriptor" 2011-06-04 RCSB TTD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TTD _pdbx_chem_comp_synonyms.name "[(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-DIHYDROXY-15A,15B-DIMETHYL-7-OXIDO-13,15,16,18-TETRAOXOHEXADECAHYDRO-1H-1,4-EPOXY-9,12-METHANO-6,8,11-TRIOXA-12A,14,17,18A-TETRAAZA-7-PHOSPHACYCLOHEXADECA[1,2,3,4-DEF]BIPHENYLEN-10-YL]METHYL DIHYDROGEN PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##