data_GDF # _chem_comp.id GDF _chem_comp.name Vinorelbine _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C45 H54 N4 O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-08-19 _chem_comp.pdbx_modified_date 2021-07-30 _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 778.932 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDF _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 7CNN _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 GDF C01 C1 C 0 1 N N N 0.822 39.380 15.627 2.032 -2.316 2.566 C01 GDF 1 GDF C02 C2 C 0 1 N N N 0.194 39.072 17.017 3.020 -1.221 2.158 C02 GDF 2 GDF C03 C3 C 0 1 N N R 1.222 38.644 18.098 3.473 -1.454 0.710 C03 GDF 3 GDF C04 C4 C 0 1 N N N 1.872 37.576 17.647 3.921 -2.868 0.870 C04 GDF 4 GDF C05 C5 C 0 1 N N N 3.282 37.392 18.046 3.578 -3.782 0.010 C05 GDF 5 GDF C06 C6 C 0 1 N N N 4.271 38.487 18.445 2.723 -3.421 -1.160 C06 GDF 6 GDF C08 C7 C 0 1 N N N 4.234 40.929 19.329 1.462 -1.683 -2.237 C08 GDF 7 GDF C09 C8 C 0 1 N N N 3.148 41.139 20.324 2.161 -0.293 -2.201 C09 GDF 8 GDF C10 C9 C 0 1 N N R 2.286 40.045 18.476 2.181 -1.262 0.006 C10 GDF 9 GDF C11 C10 C 0 1 N N R 1.935 40.675 19.736 2.024 0.062 -0.709 C11 GDF 10 GDF C12 C11 C 0 1 Y N N 1.107 41.834 19.628 0.730 0.803 -0.549 C12 GDF 11 GDF C13 C12 C 0 1 Y N N 0.954 42.750 18.571 -0.565 0.374 -0.378 C13 GDF 12 GDF C14 C13 C 0 1 Y N N 0.048 43.886 18.786 -1.551 1.349 -0.272 C14 GDF 13 GDF C15 C14 C 0 1 N N S -0.113 44.948 17.696 -3.013 0.919 -0.079 C15 GDF 14 GDF C16 C15 C 0 1 Y N N 0.257 44.410 16.221 -2.982 -0.594 -0.054 C16 GDF 15 GDF C17 C16 C 0 1 Y N N 1.228 44.971 15.293 -3.593 -1.449 -0.913 C17 GDF 16 GDF C18 C17 C 0 1 Y N N 1.179 44.181 14.099 -3.222 -2.800 -0.494 C18 GDF 17 GDF C19 C18 C 0 1 Y N N 1.892 44.222 12.886 -3.536 -4.062 -0.999 C19 GDF 18 GDF C20 C19 C 0 1 Y N N 1.639 43.324 11.837 -2.961 -5.144 -0.373 C20 GDF 19 GDF C21 C20 C 0 1 Y N N 0.646 42.325 12.022 -2.114 -4.997 0.715 C21 GDF 20 GDF C22 C21 C 0 1 Y N N -0.066 42.270 13.245 -1.800 -3.761 1.247 C22 GDF 21 GDF C23 C22 C 0 1 Y N N 0.214 43.198 14.292 -2.373 -2.650 0.627 C23 GDF 22 GDF C25 C23 C 0 1 N N N 0.658 46.126 18.304 -3.777 1.511 -1.204 C25 GDF 23 GDF C26 C24 C 0 1 N N R 2.180 45.886 18.702 -5.245 1.600 -1.199 C26 GDF 24 GDF C27 C25 C 0 1 N N N 2.822 47.235 19.014 -5.873 1.362 0.155 C27 GDF 25 GDF C28 C26 C 0 1 N N N 3.754 47.731 18.139 -6.369 0.200 0.457 C28 GDF 26 GDF C29 C27 C 0 1 N N N 4.223 49.184 18.326 -6.968 0.017 1.829 C29 GDF 27 GDF C30 C28 C 0 1 N N N 4.027 49.681 19.782 -8.479 0.251 1.760 C30 GDF 28 GDF C31 C29 C 0 1 N N N 4.262 46.886 16.827 -6.397 -0.970 -0.480 C31 GDF 29 GDF C32 C30 C 0 1 N N N 3.030 45.140 17.703 -5.971 0.737 -2.189 C32 GDF 30 GDF C34 C31 C 0 1 N N N 2.150 46.157 15.607 -4.495 -1.176 -2.092 C34 GDF 31 GDF C35 C32 C 0 1 N N N -1.622 45.354 17.567 -3.394 1.447 1.281 C35 GDF 32 GDF C37 C33 C 0 1 N N N -3.975 44.714 17.257 -3.853 3.207 2.821 C37 GDF 33 GDF C39 C34 C 0 1 Y N N -0.688 44.064 20.092 -1.244 2.697 -0.337 C39 GDF 34 GDF C41 C35 C 0 1 N N N -2.688 44.804 21.190 -1.879 4.989 -0.306 C41 GDF 35 GDF C42 C36 C 0 1 Y N N -0.508 43.095 21.160 0.064 3.143 -0.505 C42 GDF 36 GDF C43 C37 C 0 1 Y N N 0.359 42.031 20.963 1.058 2.178 -0.604 C43 GDF 37 GDF C45 C38 C 0 1 N N N 0.888 40.841 23.389 2.856 2.684 -2.091 C45 GDF 38 GDF C46 C39 C 0 1 N N S 1.032 39.860 20.759 2.995 1.120 -0.192 C46 GDF 39 GDF C47 C40 C 0 1 N N S 1.048 38.650 20.737 4.427 0.712 -0.305 C47 GDF 40 GDF C48 C41 C 0 1 N N N 0.296 38.079 21.987 5.318 1.842 0.192 C48 GDF 41 GDF C50 C42 C 0 1 N N N -1.758 37.489 23.082 7.374 3.046 0.266 C50 GDF 42 GDF C53 C43 C 0 1 N N R 0.320 38.336 19.429 4.608 -0.486 0.642 C53 GDF 43 GDF C55 C44 C 0 1 N N N -1.611 37.200 19.467 6.980 -0.748 0.676 C55 GDF 44 GDF C56 C45 C 0 1 N N N -2.457 35.911 19.720 8.259 -1.446 0.290 C56 GDF 45 GDF N07 N1 N 0 1 N N N 3.741 39.816 18.495 1.827 -2.315 -0.946 N07 GDF 46 GDF N24 N2 N 0 1 Y N N -0.320 43.389 15.591 -2.279 -1.316 0.877 N24 GDF 47 GDF N33 N3 N 0 1 N N R 3.314 45.763 16.473 -5.821 -0.676 -1.765 N33 GDF 48 GDF N44 N4 N 0 1 N N N 0.747 40.819 21.935 2.446 2.353 -0.735 N44 GDF 49 GDF O36 O1 O 0 1 N N N -2.611 44.318 17.541 -3.481 2.771 1.487 O36 GDF 50 GDF O38 O2 O 0 1 N N N -1.944 46.494 17.469 -3.621 0.679 2.186 O38 GDF 51 GDF O40 O3 O 0 1 N N N -1.589 45.147 20.354 -2.247 3.610 -0.234 O40 GDF 52 GDF O49 O4 O 0 1 N N N -1.047 38.426 22.229 6.582 1.944 -0.250 O49 GDF 53 GDF O51 O5 O 0 1 N N N 0.870 37.413 22.766 4.889 2.647 0.983 O51 GDF 54 GDF O52 O6 O 0 1 N N N 2.420 37.880 20.657 4.829 0.369 -1.628 O52 GDF 55 GDF O54 O7 O 0 1 N N N -0.194 37.087 19.399 5.802 -1.210 0.229 O54 GDF 56 GDF O57 O8 O 0 1 N N N -2.158 38.258 19.331 7.016 0.227 1.389 O57 GDF 57 GDF H1 H1 H 0 1 N N N 0.030 39.674 14.923 1.785 -2.207 3.622 H1 GDF 58 GDF H2 H2 H 0 1 N N N 1.547 40.201 15.726 1.125 -2.227 1.969 H2 GDF 59 GDF H3 H3 H 0 1 N N N 1.334 38.483 15.249 2.483 -3.294 2.397 H3 GDF 60 GDF H4 H4 H 0 1 N N N -0.322 39.977 17.371 2.536 -0.248 2.235 H4 GDF 61 GDF H5 H5 H 0 1 N N N -0.536 38.258 16.893 3.887 -1.250 2.818 H5 GDF 62 GDF H7 H7 H 0 1 N N N 1.381 36.860 17.004 4.538 -3.135 1.718 H7 GDF 63 GDF H9 H9 H 0 1 N N N 3.653 36.378 18.057 3.909 -4.802 0.143 H9 GDF 64 GDF H10 H10 H 0 1 N N N 4.662 38.242 19.444 3.376 -3.179 -1.998 H10 GDF 65 GDF H11 H11 H 0 1 N N N 4.389 41.833 18.723 0.384 -1.561 -2.316 H11 GDF 66 GDF H12 H12 H 0 1 N N N 5.175 40.656 19.829 1.845 -2.270 -3.071 H12 GDF 67 GDF H13 H13 H 0 1 N N N 3.363 40.570 21.241 3.182 -0.380 -2.546 H13 GDF 68 GDF H14 H14 H 0 1 N N N 3.063 42.208 20.567 1.600 0.410 -2.829 H14 GDF 69 GDF H15 H15 H 0 1 N N N 2.077 40.766 17.672 1.403 -1.277 0.776 H15 GDF 70 GDF H17 H17 H 0 1 N N N 1.482 42.623 17.638 -0.808 -0.677 -0.327 H17 GDF 71 GDF H18 H18 H 0 1 N N N 2.660 44.970 12.758 -4.200 -4.200 -1.843 H18 GDF 72 GDF H19 H19 H 0 1 N N N 2.188 43.391 10.909 -3.167 -6.138 -0.740 H19 GDF 73 GDF H20 H20 H 0 1 N N N 0.436 41.614 11.237 -1.677 -5.885 1.165 H20 GDF 74 GDF H21 H21 H 0 1 N N N -0.828 41.518 13.387 -1.141 -3.656 2.096 H21 GDF 75 GDF H22 H22 H 0 1 N N N 0.635 46.947 17.572 -3.388 2.556 -1.350 H22 GDF 76 GDF H23 H23 H 0 1 N N N 0.124 46.433 19.216 -3.456 1.028 -2.155 H23 GDF 77 GDF H24 H24 H 0 1 N N N 2.173 45.302 19.634 -5.507 2.649 -1.486 H24 GDF 78 GDF H25 H25 H 0 1 N N N 2.549 47.785 19.902 -5.967 2.173 0.875 H25 GDF 79 GDF H26 H26 H 0 1 N N N 5.291 49.247 18.071 -6.773 -0.996 2.178 H26 GDF 80 GDF H27 H27 H 0 1 N N N 3.646 49.832 17.650 -6.521 0.732 2.519 H27 GDF 81 GDF H28 H28 H 0 1 N N N 4.376 50.721 19.865 -8.912 0.119 2.752 H28 GDF 82 GDF H29 H29 H 0 1 N N N 2.960 49.630 20.046 -8.674 1.265 1.411 H29 GDF 83 GDF H30 H30 H 0 1 N N N 4.606 49.045 20.468 -8.926 -0.464 1.070 H30 GDF 84 GDF H31 H31 H 0 1 N N N 4.336 47.572 15.970 -5.850 -1.792 -0.031 H31 GDF 85 GDF H32 H32 H 0 1 N N N 5.253 46.459 17.042 -7.429 -1.275 -0.623 H32 GDF 86 GDF H33 H33 H 0 1 N N N 3.993 44.926 18.190 -7.028 1.013 -2.197 H33 GDF 87 GDF H34 H34 H 0 1 N N N 2.515 44.195 17.478 -5.541 0.878 -3.175 H34 GDF 88 GDF H35 H35 H 0 1 N N N 2.535 46.565 14.661 -4.010 -0.478 -2.758 H35 GDF 89 GDF H36 H36 H 0 1 N N N 1.567 46.930 16.129 -4.623 -2.115 -2.642 H36 GDF 90 GDF H37 H37 H 0 1 N N N -4.625 43.827 17.268 -3.887 4.296 2.851 H37 GDF 91 GDF H38 H38 H 0 1 N N N -4.316 45.428 18.021 -4.834 2.806 3.075 H38 GDF 92 GDF H39 H39 H 0 1 N N N -4.020 45.189 16.266 -3.116 2.847 3.540 H39 GDF 93 GDF H40 H40 H 0 1 N N N -3.326 45.688 21.339 -1.400 5.187 -1.265 H40 GDF 94 GDF H41 H41 H 0 1 N N N -3.275 44.004 20.714 -2.770 5.608 -0.210 H41 GDF 95 GDF H42 H42 H 0 1 N N N -2.313 44.454 22.163 -1.185 5.223 0.502 H42 GDF 96 GDF H43 H43 H 0 1 N N N -1.041 43.202 22.093 0.297 4.196 -0.553 H43 GDF 97 GDF H44 H44 H 0 1 N N N 1.164 39.838 23.746 2.375 3.612 -2.400 H44 GDF 98 GDF H45 H45 H 0 1 N N N 1.672 41.559 23.670 3.939 2.808 -2.123 H45 GDF 99 GDF H46 H46 H 0 1 N N N -0.066 41.143 23.845 2.562 1.880 -2.766 H46 GDF 100 GDF H47 H47 H 0 1 N N N 0.079 40.018 20.234 2.803 1.202 0.914 H47 GDF 101 GDF H48 H48 H 0 1 N N N -2.794 37.832 23.220 7.448 2.964 1.350 H48 GDF 102 GDF H49 H49 H 0 1 N N N -1.760 36.495 22.612 8.372 3.012 -0.171 H49 GDF 103 GDF H50 H50 H 0 1 N N N -1.258 37.431 24.060 6.895 3.990 0.006 H50 GDF 104 GDF H51 H51 H 0 1 N N N -0.516 39.049 19.372 4.788 -0.097 1.649 H51 GDF 105 GDF H52 H52 H 0 1 N N N -3.526 36.171 19.740 8.645 -1.012 -0.632 H52 GDF 106 GDF H53 H53 H 0 1 N N N -2.272 35.187 18.913 8.994 -1.324 1.086 H53 GDF 107 GDF H54 H54 H 0 1 N N N -2.169 35.467 20.685 8.061 -2.507 0.137 H54 GDF 108 GDF H55 H55 H 0 1 N N N -1.044 42.824 15.987 -1.789 -0.923 1.613 H55 GDF 109 GDF H57 H57 H 0 1 N N N 2.514 37.319 21.418 5.757 0.104 -1.700 H57 GDF 110 GDF H58 H58 H 0 1 N N N 5.095 38.479 17.717 2.129 -4.294 -1.433 H58 GDF 111 # # 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 GDF C01 C02 SING N N 1 GDF C02 C03 SING N N 2 GDF C03 C04 SING N N 3 GDF C03 C53 SING N N 4 GDF C04 C05 DOUB N N 5 GDF C05 C06 SING N N 6 GDF C06 N07 SING N N 7 GDF C08 C09 SING N N 8 GDF C08 N07 SING N N 9 GDF C09 C11 SING N N 10 GDF C10 C11 SING N N 11 GDF C10 N07 SING N N 12 GDF C11 C12 SING N N 13 GDF C11 C46 SING N N 14 GDF C12 C13 DOUB Y N 15 GDF C12 C43 SING Y N 16 GDF C13 C14 SING Y N 17 GDF C14 C15 SING N N 18 GDF C14 C39 DOUB Y N 19 GDF C15 C16 SING N N 20 GDF C15 C25 SING N N 21 GDF C15 C35 SING N N 22 GDF C16 C17 DOUB Y N 23 GDF C16 N24 SING Y N 24 GDF C17 C18 SING Y N 25 GDF C17 C34 SING N N 26 GDF C18 C19 DOUB Y N 27 GDF C18 C23 SING Y N 28 GDF C19 C20 SING Y N 29 GDF C20 C21 DOUB Y N 30 GDF C21 C22 SING Y N 31 GDF C22 C23 DOUB Y N 32 GDF C23 N24 SING Y N 33 GDF C25 C26 SING N N 34 GDF C26 C27 SING N N 35 GDF C26 C32 SING N N 36 GDF C27 C28 DOUB N N 37 GDF C28 C29 SING N N 38 GDF C28 C31 SING N N 39 GDF C29 C30 SING N N 40 GDF C31 N33 SING N N 41 GDF C32 N33 SING N N 42 GDF C34 N33 SING N N 43 GDF C35 O36 SING N N 44 GDF C35 O38 DOUB N N 45 GDF C37 O36 SING N N 46 GDF C39 C42 SING Y N 47 GDF C39 O40 SING N N 48 GDF C41 O40 SING N N 49 GDF C42 C43 DOUB Y N 50 GDF C43 N44 SING N N 51 GDF C45 N44 SING N N 52 GDF C46 C47 SING N N 53 GDF C46 N44 SING N N 54 GDF C47 C48 SING N N 55 GDF C47 C53 SING N N 56 GDF C47 O52 SING N N 57 GDF C48 O49 SING N N 58 GDF C48 O51 DOUB N N 59 GDF C50 O49 SING N N 60 GDF C53 O54 SING N N 61 GDF C55 C56 SING N N 62 GDF C55 O54 SING N N 63 GDF C55 O57 DOUB N N 64 GDF C01 H1 SING N N 65 GDF C01 H2 SING N N 66 GDF C01 H3 SING N N 67 GDF C02 H4 SING N N 68 GDF C02 H5 SING N N 69 GDF C04 H7 SING N N 70 GDF C05 H9 SING N N 71 GDF C06 H10 SING N N 72 GDF C08 H11 SING N N 73 GDF C08 H12 SING N N 74 GDF C09 H13 SING N N 75 GDF C09 H14 SING N N 76 GDF C10 H15 SING N N 77 GDF C13 H17 SING N N 78 GDF C19 H18 SING N N 79 GDF C20 H19 SING N N 80 GDF C21 H20 SING N N 81 GDF C22 H21 SING N N 82 GDF C25 H22 SING N N 83 GDF C25 H23 SING N N 84 GDF C26 H24 SING N N 85 GDF C27 H25 SING N N 86 GDF C29 H26 SING N N 87 GDF C29 H27 SING N N 88 GDF C30 H28 SING N N 89 GDF C30 H29 SING N N 90 GDF C30 H30 SING N N 91 GDF C31 H31 SING N N 92 GDF C31 H32 SING N N 93 GDF C32 H33 SING N N 94 GDF C32 H34 SING N N 95 GDF C34 H35 SING N N 96 GDF C34 H36 SING N N 97 GDF C37 H37 SING N N 98 GDF C37 H38 SING N N 99 GDF C37 H39 SING N N 100 GDF C41 H40 SING N N 101 GDF C41 H41 SING N N 102 GDF C41 H42 SING N N 103 GDF C42 H43 SING N N 104 GDF C45 H44 SING N N 105 GDF C45 H45 SING N N 106 GDF C45 H46 SING N N 107 GDF C46 H47 SING N N 108 GDF C50 H48 SING N N 109 GDF C50 H49 SING N N 110 GDF C50 H50 SING N N 111 GDF C53 H51 SING N N 112 GDF C56 H52 SING N N 113 GDF C56 H53 SING N N 114 GDF C56 H54 SING N N 115 GDF N24 H55 SING N N 116 GDF O52 H57 SING N N 117 GDF C06 H58 SING N N 118 GDF C10 C03 SING N N 119 # # 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 GDF InChI InChI 1.03 "InChI=1S/C45H54N4O8/c1-8-27-19-28-22-44(40(51)55-6,36-30(25-48(23-27)24-28)29-13-10-11-14-33(29)46-36)32-20-31-34(21-35(32)54-5)47(4)38-43(31)16-18-49-17-12-15-42(9-2,37(43)49)39(57-26(3)50)45(38,53)41(52)56-7/h10-15,19-21,28,37-39,46,53H,8-9,16-18,22-25H2,1-7H3/t28-,37-,38-,39+,42+,43+,44-,45-/m0/s1" GDF InChIKey InChI 1.03 GBABOYUKABKIAF-SULIYOFUSA-N GDF SMILES_CANONICAL CACTVS 3.385 "CCC1=C[C@@H]2C[N@](C1)Cc3c([nH]c4ccccc34)[C@@](C2)(C(=O)OC)c5cc6c(cc5OC)N(C)[C@@H]7[C@](O)([C@H](OC(C)=O)[C@]8(CC)C=CCN9CC[C@]67[C@H]89)C(=O)OC" GDF SMILES CACTVS 3.385 "CCC1=C[CH]2C[N](C1)Cc3c([nH]c4ccccc34)[C](C2)(C(=O)OC)c5cc6c(cc5OC)N(C)[CH]7[C](O)([CH](OC(C)=O)[C]8(CC)C=CCN9CC[C]67[CH]89)C(=O)OC" GDF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC1=C[C@H]2C[C@@](c3c(c4ccccc4[nH]3)C[N@](C2)C1)(c5cc6c(cc5OC)N([C@H]7[C@]68CC[N@@]9C8[C@@](C=CC9)([C@H]([C@@]7(C(=O)OC)O)OC(=O)C)CC)C)C(=O)OC" GDF SMILES "OpenEye OEToolkits" 2.0.7 "CCC1=CC2CC(c3c(c4ccccc4[nH]3)CN(C2)C1)(c5cc6c(cc5OC)N(C7C68CCN9C8C(C=CC9)(C(C7(C(=O)OC)O)OC(=O)C)CC)C)C(=O)OC" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GDF "Create component" 2020-08-19 PDBJ GDF "Modify linking type" 2020-08-21 PDBJ GDF "Initial release" 2021-08-04 RCSB ##