data_WUH # _chem_comp.id WUH _chem_comp.name "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 TTD _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -2 _chem_comp.pdbx_initial_date 2023-05-18 _chem_comp.pdbx_modified_date 2023-11-17 _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 TT _chem_comp.three_letter_code WUH _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8OY4 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 WUH C1R C1 C 0 1 N N R N N N 26.699 12.954 4.456 0.386 0.374 -0.530 C1R WUH 1 WUH C1 C2 C 0 1 N N R N N N 23.047 11.682 6.053 -3.292 0.216 -0.710 C1 WUH 2 WUH C2T C3 C 0 1 N N N N N N 25.180 14.746 4.021 1.280 -1.902 -0.371 C2T WUH 3 WUH C2R C4 C 0 1 N N N N N N 26.966 11.466 4.448 0.318 1.343 0.657 C2R WUH 4 WUH C3 C5 C 0 1 N N N N N N 22.885 10.186 6.200 -4.699 0.885 -0.581 C3 WUH 5 WUH C7 C6 C 0 1 N N N N N N 21.977 13.382 4.721 -4.435 -1.764 0.005 C7 WUH 6 WUH "C3'" C7 C 0 1 N N S N N N 23.553 9.947 7.565 -4.396 2.379 -0.883 "C3'" WUH 7 WUH C3R C8 C 0 1 N N S N N N 28.455 11.444 4.796 1.578 2.214 0.556 C3R WUH 8 WUH C4T C9 C 0 1 N N N N N N 23.755 14.752 2.099 0.755 -3.111 1.665 C4T WUH 9 WUH "C4'" C10 C 0 1 N N R N N N 24.400 11.208 7.790 -2.864 2.500 -0.804 "C4'" WUH 10 WUH C4R C11 C 0 1 N N R N N N 28.988 12.683 4.080 2.432 1.547 -0.536 C4R WUH 11 WUH C2 C12 C 0 1 N N N N N N 21.381 12.797 2.412 -3.241 -3.795 -0.609 C2 WUH 12 WUH C5T C13 C 0 1 N N N N N N 24.263 13.493 1.759 -0.389 -2.465 1.949 C5T WUH 13 WUH C5R C14 C 0 1 N N N N N N 29.694 12.402 2.779 3.613 0.815 0.102 C5R WUH 14 WUH C5A C15 C 0 1 N N N N N N 24.394 12.988 0.350 -1.155 -2.695 3.232 C5A WUH 15 WUH C5M C16 C 0 1 N N N N N N 22.157 10.651 1.565 -0.774 -4.014 -1.024 C5M WUH 16 WUH C4 C17 C 0 1 N N N N N N 25.831 10.988 8.208 -2.481 3.635 0.126 C4 WUH 17 WUH C8 C18 C 0 1 N N N N N N 22.303 11.741 2.494 -1.985 -3.293 -0.503 C8 WUH 18 WUH C6T C19 C 0 1 N N R N N N 24.686 12.595 2.901 -0.798 -1.445 0.832 C6T WUH 19 WUH C5 C20 C 0 1 N N S N N N 23.453 11.784 3.514 -2.057 -1.943 0.232 C5 WUH 20 WUH N1T N1 N 0 1 N N N N N N 25.489 13.438 3.802 0.301 -1.007 -0.045 N1T WUH 21 WUH N2 N2 N 0 1 N N N N N N 22.833 12.307 4.744 -3.206 -1.104 -0.163 N2 WUH 22 WUH N3T N3 N 0 1 N N N N N N 24.069 15.221 3.367 1.506 -2.888 0.526 N3T WUH 23 WUH N1 N4 N 0 1 N N N N N N 21.431 13.653 3.499 -4.357 -3.097 -0.195 N1 WUH 24 WUH O2T O1 O 0 1 N N N N N N 25.860 15.472 4.729 1.954 -1.801 -1.378 O2T WUH 25 WUH O1 O2 O 0 1 N N N N N N 21.681 14.032 5.712 -5.494 -1.235 0.252 O1 WUH 26 WUH "O3'" O3 O 0 1 N N N N N N 22.574 9.906 8.599 -4.853 2.719 -2.194 "O3'" WUH 27 WUH O3R O4 O 0 1 N N N N N N 28.656 11.401 6.254 1.259 3.560 0.182 O3R WUH 28 WUH O4T O5 O -1 1 N N N N N N 23.044 15.471 1.360 1.199 -4.040 2.553 O4T WUH 29 WUH O4R O6 O 0 1 N N N N N N 27.834 13.524 3.829 1.597 0.620 -1.230 O4R WUH 30 WUH O5P O7 O 0 1 N N N N N N 28.385 8.819 6.506 -0.387 3.760 2.095 O5P WUH 31 WUH O2 O8 O 0 1 N N N N N N 24.346 11.925 6.539 -2.367 1.236 -0.301 O2 WUH 32 WUH O3 O9 O -1 1 N N N N N N 20.555 12.979 1.516 -3.396 -5.033 -1.144 O3 WUH 33 WUH O5R O10 O 0 1 N N N N N N 30.847 11.586 3.034 4.463 0.298 -0.923 O5R WUH 34 WUH O4P O11 O 0 1 N N N N N N 28.443 10.339 8.561 0.366 5.901 0.989 O4P WUH 35 WUH O4 O12 O 0 1 N N N N N N 26.502 10.381 7.085 -1.234 4.214 -0.250 O4 WUH 36 WUH OP1 O13 O 0 1 N N N N N N 32.531 12.455 1.337 6.685 0.264 0.275 OP1 WUH 37 WUH OP2 O14 O 0 1 N N N N N N 32.437 13.429 3.671 5.426 -1.918 0.115 OP2 WUH 38 WUH PB P1 P 0 1 N N N N N N 32.335 12.186 2.811 5.807 -0.532 -0.611 PB WUH 39 WUH P1 P2 P 0 1 N N N N N N 28.075 10.125 7.149 -0.007 4.346 0.792 P1 WUH 40 WUH H1R H1 H 0 1 N N N N N N 26.675 13.280 5.506 -0.466 0.513 -1.193 H1R WUH 41 WUH H2 H2 H 0 1 N N N N N N 22.334 12.144 6.752 -3.170 0.099 -1.826 H2 WUH 42 WUH H2R1 H3 H 0 0 N N N N N N 26.365 10.942 5.206 -0.576 1.958 0.590 H2R1 WUH 43 WUH H2R2 H4 H 0 0 N N N N N N 26.774 11.025 3.459 0.325 0.788 1.597 H2R2 WUH 44 WUH H3 H5 H 0 1 N N N N N N 21.824 9.895 6.213 -5.393 0.481 -1.312 H3 WUH 45 WUH H4 H6 H 0 1 N N N N N N 23.404 9.643 5.396 -5.083 0.785 0.435 H4 WUH 46 WUH H1 H7 H 0 1 N N N N N N 24.185 9.047 7.542 -4.869 3.019 -0.140 H1 WUH 47 WUH H3R H8 H 0 1 N N N N N N 28.909 10.552 4.339 2.120 2.241 1.498 H3R WUH 48 WUH "H4'" H9 H 0 1 N N N N N N 23.906 11.809 8.567 -2.473 2.661 -1.814 "H4'" WUH 49 WUH H4R H10 H 0 1 N N N N N N 29.683 13.204 4.755 2.798 2.307 -1.226 H4R WUH 50 WUH H5R1 H12 H 0 0 N N N N N N 30.009 13.350 2.319 4.176 1.510 0.726 H5R1 WUH 51 WUH H5R2 H13 H 0 0 N N N N N N 29.012 11.873 2.097 3.243 -0.006 0.716 H5R2 WUH 52 WUH H5A1 H14 H 0 0 N N N N N N 24.820 11.974 0.362 -0.634 -3.435 3.839 H5A1 WUH 53 WUH H5A2 H15 H 0 0 N N N N N N 23.402 12.964 -0.124 -1.227 -1.758 3.784 H5A2 WUH 54 WUH H5A3 H16 H 0 0 N N N N N N 25.056 13.657 -0.219 -2.156 -3.057 2.997 H5A3 WUH 55 WUH H71 H17 H 0 1 N N N N N N 22.944 9.905 1.748 -1.079 -4.958 -1.474 H71 WUH 56 WUH H72 H18 H 0 1 N N N N N N 21.170 10.184 1.700 -0.278 -3.397 -1.773 H72 WUH 57 WUH H73 H19 H 0 1 N N N N N N 22.245 11.032 0.537 -0.086 -4.209 -0.201 H73 WUH 58 WUH H5 H20 H 0 1 N N N N N N 25.873 10.320 9.081 -3.254 4.404 0.083 H5 WUH 59 WUH H7 H21 H 0 1 N N N N N N 26.305 11.949 8.459 -2.414 3.256 1.146 H7 WUH 60 WUH H6T H23 H 0 1 N N N N N N 25.361 11.838 2.475 -1.021 -0.545 1.442 H6T WUH 61 WUH H8 H24 H 0 1 N N N N N N 23.792 10.753 3.694 -2.581 -2.372 1.158 H8 WUH 62 WUH HN3 H25 H 0 1 N N N N N N 23.486 15.905 3.805 2.255 -3.484 0.355 HN3 WUH 63 WUH HT H26 H 0 1 N N N N N N 21.027 14.560 3.377 -5.166 -3.605 -0.028 HT WUH 64 WUH "HO3'" H27 H 0 0 N Y N N N N 23.001 9.758 9.435 -5.806 2.616 -2.318 "HO3'" WUH 65 WUH H4P H28 H 0 1 N N N N N N 28.861 9.557 8.902 -0.354 6.435 1.354 H4P WUH 66 WUH HOP2 H30 H 0 0 N N N N N N 32.611 14.183 3.120 4.852 -2.492 -0.410 HOP2 WUH 67 WUH OP3 O15 O 0 1 N Y N N N N ? ? ? 6.578 -0.843 -1.990 OP3 WUH 68 WUH HOP3 H31 H 0 0 N N N N N N ? ? ? 7.399 -1.342 -1.879 HOP3 WUH 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 WUH C5A C5T SING N N 1 WUH OP1 PB DOUB N N 2 WUH O4T C4T SING N N 3 WUH O3 C2 SING N N 4 WUH C5M C8 SING N N 5 WUH C5T C4T DOUB N N 6 WUH C5T C6T SING N N 7 WUH C4T N3T SING N N 8 WUH C2 C8 DOUB N N 9 WUH C2 N1 SING N N 10 WUH C8 C5 SING N N 11 WUH C5R O5R SING N N 12 WUH C5R C4R SING N N 13 WUH PB O5R SING N N 14 WUH PB OP2 SING N N 15 WUH C6T C5 SING N N 16 WUH C6T N1T SING N N 17 WUH N3T C2T SING N N 18 WUH N1 C7 SING N N 19 WUH C5 N2 SING N N 20 WUH N1T C2T SING N N 21 WUH N1T C1R SING N N 22 WUH O4R C4R SING N N 23 WUH O4R C1R SING N N 24 WUH C2T O2T DOUB N N 25 WUH C4R C3R SING N N 26 WUH C2R C1R SING N N 27 WUH C2R C3R SING N N 28 WUH C7 N2 SING N N 29 WUH C7 O1 DOUB N N 30 WUH N2 C1 SING N N 31 WUH C3R O3R SING N N 32 WUH C1 C3 SING N N 33 WUH C1 O2 SING N N 34 WUH C3 "C3'" SING N N 35 WUH O3R P1 SING N N 36 WUH O5P P1 DOUB N N 37 WUH O2 "C4'" SING N N 38 WUH O4 P1 SING N N 39 WUH O4 C4 SING N N 40 WUH P1 O4P SING N N 41 WUH "C3'" "C4'" SING N N 42 WUH "C3'" "O3'" SING N N 43 WUH "C4'" C4 SING N N 44 WUH C1R H1R SING N N 45 WUH C1 H2 SING N N 46 WUH C2R H2R1 SING N N 47 WUH C2R H2R2 SING N N 48 WUH C3 H3 SING N N 49 WUH C3 H4 SING N N 50 WUH "C3'" H1 SING N N 51 WUH C3R H3R SING N N 52 WUH "C4'" "H4'" SING N N 53 WUH C4R H4R SING N N 54 WUH C5R H5R1 SING N N 55 WUH C5R H5R2 SING N N 56 WUH C5A H5A1 SING N N 57 WUH C5A H5A2 SING N N 58 WUH C5A H5A3 SING N N 59 WUH C5M H71 SING N N 60 WUH C5M H72 SING N N 61 WUH C5M H73 SING N N 62 WUH C4 H5 SING N N 63 WUH C4 H7 SING N N 64 WUH C6T H6T SING N N 65 WUH C5 H8 SING N N 66 WUH N3T HN3 SING N N 67 WUH N1 HT SING N N 68 WUH "O3'" "HO3'" SING N N 69 WUH O4P H4P SING N N 70 WUH OP2 HOP2 SING N N 71 WUH PB OP3 SING N N 72 WUH OP3 HOP3 SING N N 73 # 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 WUH InChI InChI 1.06 "InChI=1S/C20H30N4O15P2/c1-7-15-16-8(2)18(27)22-20(29)24(16)14-4-10(12(38-14)6-35-40(30,31)32)39-41(33,34)36-5-11-9(25)3-13(37-11)23(15)19(28)21-17(7)26/h9-16,25-27H,3-6H2,1-2H3,(H,21,28)(H,22,29)(H,33,34)(H2,30,31,32)/p-2/t9-,10-,11+,12+,13+,14+,15-,16+/m0/s1" WUH InChIKey InChI 1.06 MLKSHAMOXDJESO-BIELKLQGSA-L WUH SMILES_CANONICAL CACTVS 3.385 "CC1=C([O-])NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[C@H]4C[C@@H](O[C@@H]4CO[P](O)(O)=O)N5[C@@H]([C@H]12)C(=C([O-])NC5=O)C)O3" WUH SMILES CACTVS 3.385 "CC1=C([O-])NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[CH]4C[CH](O[CH]4CO[P](O)(O)=O)N5[CH]([CH]12)C(=C([O-])NC5=O)C)O3" WUH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=C(NC(=O)N2[C@@H]1[C@H]3C(=C(NC(=O)N3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)OP(=O)(OC[C@@H]5[C@H](C[C@H]2O5)O)O)[O-])C)[O-]" WUH SMILES "OpenEye OEToolkits" 2.0.7 "CC1=C(NC(=O)N2C1C3C(=C(NC(=O)N3C4CC(C(O4)COP(=O)(O)O)OP(=O)(OCC5C(CC2O5)O)O)[O-])C)[O-]" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site WUH "Create component" 2023-05-18 PDBE WUH "Modify aromatic_flag" 2023-05-19 PDBE WUH "Modify aromatic_flag" 2023-05-22 PDBE WUH "Initial release" 2023-11-22 RCSB #