data_77Y # _chem_comp.id 77Y _chem_comp.name ; 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C22 H25 N4 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-09-12 _chem_comp.pdbx_modified_date 2016-09-23 _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 520.429 _chem_comp.one_letter_code U _chem_comp.three_letter_code 77Y _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 5LUW _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 77Y C6 C1 C 0 1 N N N -29.328 37.751 6.750 1.230 -1.073 0.935 C6 77Y 1 77Y C1 C2 C 0 1 N N N -28.193 35.784 8.842 -2.199 -1.618 -0.243 C1 77Y 2 77Y C29 C3 C 0 1 Y N N -30.791 30.792 6.827 -8.808 3.053 1.523 C29 77Y 3 77Y C28 C4 C 0 1 Y N N -30.854 29.423 6.635 -10.148 2.728 1.683 C28 77Y 4 77Y C27 C5 C 0 1 Y N N -30.480 28.508 7.624 -10.699 1.663 1.003 C27 77Y 5 77Y C30 C6 C 0 1 Y N N -30.345 31.191 8.087 -8.011 2.322 0.687 C30 77Y 6 77Y C5 C7 C 0 1 N N N -29.265 37.955 8.140 0.194 -1.381 0.101 C5 77Y 7 77Y C4 C8 C 0 1 N N N -30.162 38.978 8.675 0.509 -1.887 -1.243 C4 77Y 8 77Y C3 C9 C 0 1 N N N -27.525 34.914 9.838 -3.622 -1.549 0.249 C3 77Y 9 77Y C2 C10 C 0 1 N N N -31.010 39.458 6.584 2.781 -1.706 -0.729 C2 77Y 10 77Y C14 C11 C 0 1 Y N N -30.003 28.902 8.862 -9.906 0.906 0.147 C14 77Y 11 77Y C16 C12 C 0 1 Y N N -29.183 29.208 10.897 -9.005 -0.554 -1.304 C16 77Y 12 77Y O34 O1 O 0 1 N N N -27.089 32.146 10.001 -6.256 -1.051 0.530 O34 77Y 13 77Y C32 C13 C 0 1 N N N -28.108 32.690 10.464 -5.744 -0.591 -0.469 C32 77Y 14 77Y C33 C14 C 0 1 N N N -29.197 31.787 11.100 -6.577 0.195 -1.448 C33 77Y 15 77Y C12 C15 C 0 1 Y N N -29.382 30.507 10.345 -7.999 0.264 -0.956 C12 77Y 16 77Y N15 N1 N 0 1 Y N N -29.586 28.296 9.981 -10.151 -0.188 -0.652 N15 77Y 17 77Y C13 C16 C 0 1 Y N N -29.957 30.317 9.052 -8.547 1.237 -0.007 C13 77Y 18 77Y N9 N2 N 0 1 N N N -28.479 33.938 10.423 -4.431 -0.785 -0.703 N9 77Y 19 77Y C7 C17 C 0 1 N N N -28.521 37.092 9.045 -1.207 -1.210 0.537 C7 77Y 20 77Y O4 O2 O 0 1 N N N -30.125 39.179 9.944 -0.381 -2.175 -2.023 O4 77Y 21 77Y N3 N3 N 0 1 N N N -30.967 39.681 7.897 1.804 -2.026 -1.595 N3 77Y 22 77Y O2 O3 O 0 1 N N N -31.756 40.084 5.846 3.941 -1.839 -1.070 O2 77Y 23 77Y N1 N4 N 0 1 N N N -30.167 38.517 6.031 2.514 -1.236 0.501 N1 77Y 24 77Y "C1'" C18 C 0 1 N N R -30.258 38.231 4.575 3.623 -0.905 1.399 "C1'" 77Y 25 77Y "C2'" C19 C 0 1 N N N -28.870 38.343 3.758 4.413 -2.181 1.748 "C2'" 77Y 26 77Y "C3'" C20 C 0 1 N N S -29.298 37.371 2.713 5.854 -1.878 1.269 "C3'" 77Y 27 77Y "O3'" O4 O 0 1 N N N -30.050 38.141 1.857 6.817 -2.356 2.210 "O3'" 77Y 28 77Y "O4'" O5 O 0 1 N N N -30.602 36.852 4.452 4.530 -0.003 0.743 "O4'" 77Y 29 77Y "C4'" C21 C 0 1 N N R -29.963 36.180 3.360 5.858 -0.329 1.212 "C4'" 77Y 30 77Y "C5'" C22 C 0 1 N N N -29.081 35.084 3.768 6.916 0.171 0.227 "C5'" 77Y 31 77Y "O5'" O6 O 0 1 N N N -27.966 35.629 4.509 6.979 1.598 0.279 "O5'" 77Y 32 77Y P P1 P 0 1 N N N -26.573 35.038 4.024 7.987 2.465 -0.629 P 77Y 33 77Y OP1 O7 O 0 1 N N N -26.465 34.858 2.556 7.784 2.124 -2.055 OP1 77Y 34 77Y OP2 O8 O 0 1 N N N -25.602 35.970 4.776 7.695 4.033 -0.406 OP2 77Y 35 77Y H1 H1 H 0 1 N N N -28.718 36.998 6.272 1.036 -0.698 1.929 H1 77Y 36 77Y H2 H2 H 0 1 N N N -28.438 35.350 7.884 -1.987 -2.000 -1.231 H2 77Y 37 77Y H3 H3 H 0 1 N N N -31.067 31.499 6.058 -8.393 3.893 2.060 H3 77Y 38 77Y H4 H4 H 0 1 N N N -31.205 29.047 5.685 -10.765 3.315 2.348 H4 77Y 39 77Y H5 H5 H 0 1 N N N -30.567 27.452 7.414 -11.742 1.418 1.135 H5 77Y 40 77Y H6 H6 H 0 1 N N N -30.306 32.248 8.306 -6.971 2.584 0.564 H6 77Y 41 77Y H7 H7 H 0 1 N N N -26.708 34.366 9.346 -4.024 -2.558 0.339 H7 77Y 42 77Y H8 H8 H 0 1 N N N -27.113 35.540 10.643 -3.646 -1.059 1.222 H8 77Y 43 77Y H9 H9 H 0 1 N N N -28.781 28.989 11.875 -8.922 -1.380 -1.995 H9 77Y 44 77Y H10 H10 H 0 1 N N N -30.151 32.335 11.108 -6.174 1.204 -1.539 H10 77Y 45 77Y H11 H11 H 0 1 N N N -28.902 31.550 12.133 -6.552 -0.295 -2.421 H11 77Y 46 77Y H12 H12 H 0 1 N N N -29.574 27.306 10.121 -11.008 -0.634 -0.739 H12 77Y 47 77Y H13 H13 H 0 1 N N N -29.371 34.227 10.772 -4.022 -0.417 -1.502 H13 77Y 48 77Y H14 H14 H 0 1 N N N -28.194 37.534 9.975 -1.423 -0.754 1.492 H14 77Y 49 77Y H15 H15 H 0 1 N N N -31.550 40.388 8.298 2.032 -2.362 -2.476 H15 77Y 50 77Y H16 H16 H 0 1 N N N -31.007 38.879 4.098 3.237 -0.447 2.310 H16 77Y 51 77Y H17 H17 H 0 1 N N N -27.997 38.004 4.335 4.398 -2.357 2.823 H17 77Y 52 77Y H18 H18 H 0 1 N N N -28.679 39.351 3.362 4.005 -3.040 1.215 H18 77Y 53 77Y H19 H19 H 0 1 N N N -28.398 37.012 2.192 6.032 -2.304 0.282 H19 77Y 54 77Y H20 H20 H 0 1 N N N -29.518 38.853 1.520 6.852 -3.320 2.281 H20 77Y 55 77Y H21 H21 H 0 1 N N N -30.727 35.790 2.671 6.029 0.091 2.203 H21 77Y 56 77Y H22 H22 H 0 1 N N N -29.638 34.380 4.404 7.887 -0.245 0.493 H22 77Y 57 77Y H23 H23 H 0 1 N N N -28.709 34.558 2.876 6.650 -0.143 -0.783 H23 77Y 58 77Y H25 H25 H 0 1 N N N -24.992 36.357 4.159 8.267 4.617 -0.923 H25 77Y 59 77Y OP3 OP3 O 0 1 N Y N -26.412 33.648 4.706 9.505 2.137 -0.208 OP3 77Y 60 77Y H27 H27 H 0 1 N N N -26.279 32.982 4.041 9.710 2.336 0.715 H27 77Y 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 77Y "O3'" "C3'" SING N N 1 77Y OP1 P DOUB N N 2 77Y "C3'" "C4'" SING N N 3 77Y "C3'" "C2'" SING N N 4 77Y "C4'" "C5'" SING N N 5 77Y "C4'" "O4'" SING N N 6 77Y "C2'" "C1'" SING N N 7 77Y "C5'" "O5'" SING N N 8 77Y P "O5'" SING N N 9 77Y P OP2 SING N N 10 77Y "O4'" "C1'" SING N N 11 77Y "C1'" N1 SING N N 12 77Y O2 C2 DOUB N N 13 77Y N1 C2 SING N N 14 77Y N1 C6 SING N N 15 77Y C2 N3 SING N N 16 77Y C28 C29 DOUB Y N 17 77Y C28 C27 SING Y N 18 77Y C6 C5 DOUB N N 19 77Y C29 C30 SING Y N 20 77Y C27 C14 DOUB Y N 21 77Y N3 C4 SING N N 22 77Y C30 C13 DOUB Y N 23 77Y C5 C4 SING N N 24 77Y C5 C7 SING N N 25 77Y C4 O4 DOUB N N 26 77Y C1 C7 DOUB N E 27 77Y C1 C3 SING N N 28 77Y C14 C13 SING Y N 29 77Y C14 N15 SING Y N 30 77Y C13 C12 SING Y N 31 77Y C3 N9 SING N N 32 77Y N15 C16 SING Y N 33 77Y O34 C32 DOUB N N 34 77Y C12 C16 DOUB Y N 35 77Y C12 C33 SING N N 36 77Y N9 C32 SING N N 37 77Y C32 C33 SING N N 38 77Y C6 H1 SING N N 39 77Y C1 H2 SING N N 40 77Y C29 H3 SING N N 41 77Y C28 H4 SING N N 42 77Y C27 H5 SING N N 43 77Y C30 H6 SING N N 44 77Y C3 H7 SING N N 45 77Y C3 H8 SING N N 46 77Y C16 H9 SING N N 47 77Y C33 H10 SING N N 48 77Y C33 H11 SING N N 49 77Y N15 H12 SING N N 50 77Y N9 H13 SING N N 51 77Y C7 H14 SING N N 52 77Y N3 H15 SING N N 53 77Y "C1'" H16 SING N N 54 77Y "C2'" H17 SING N N 55 77Y "C2'" H18 SING N N 56 77Y "C3'" H19 SING N N 57 77Y "O3'" H20 SING N N 58 77Y "C4'" H21 SING N N 59 77Y "C5'" H22 SING N N 60 77Y "C5'" H23 SING N N 61 77Y OP2 H25 SING N N 62 77Y P OP3 SING N N 63 77Y OP3 H27 SING N N 64 # 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 77Y InChI InChI 1.03 "InChI=1S/C22H25N4O9P/c27-17-9-20(35-18(17)12-34-36(31,32)33)26-11-13(21(29)25-22(26)30)4-3-7-23-19(28)8-14-10-24-16-6-2-1-5-15(14)16/h1-6,10-11,17-18,20,24,27H,7-9,12H2,(H,23,28)(H,25,29,30)(H2,31,32,33)/b4-3+/t17-,18+,20+/m0/s1" 77Y InChIKey InChI 1.03 DJBPRNKHEIKONB-VGEFNSAVSA-N 77Y SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(/C=C/CNC(=O)Cc3c[nH]c4ccccc34)C(=O)NC2=O" 77Y SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=CCNC(=O)Cc3c[nH]c4ccccc34)C(=O)NC2=O" 77Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "c1ccc2c(c1)c(c[nH]2)CC(=O)NC/C=C/C3=CN(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" 77Y SMILES "OpenEye OEToolkits" 2.0.5 "c1ccc2c(c1)c(c[nH]2)CC(=O)NCC=CC3=CN(C(=O)NC3=O)C4CC(C(O4)COP(=O)(O)O)O" # 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 77Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-[2-(1~{H}-indol-3-yl)ethanoylamino]prop-1-enyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-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 77Y "Create component" 2016-09-12 EBI 77Y "Other modification" 2016-09-13 EBI 77Y "Initial release" 2016-09-28 RCSB #