data_PRDCC_001016 # _chem_comp.id PRD_001016 _chem_comp.name Glidobactin _chem_comp.formula "C27 H46 N4 O6" _chem_comp.formula_weight 522.677 _chem_comp.pdbx_release_status REF_ONLY _chem_comp.type peptide-like _chem_comp.pdbx_type ? _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date ? _chem_comp.pdbx_modified_date ? _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag ? _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag ? _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site ? # 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_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag PRD_001016 C1 C1 C 0 1 N N N 58.726 -134.579 35.374 1.846 -0.862 0.279 MH9 1 C polymer 1 1 1 ? ? ? PRD_001016 O1 O1 O 0 1 N N N 58.384 -135.334 36.291 1.844 -1.592 1.253 MH9 1 O polymer 1 1 2 ? ? ? PRD_001016 C2 C2 C 0 1 N N N 57.646 -133.907 34.603 3.101 -0.571 -0.414 MH9 1 C1 polymer 1 1 3 ? ? ? PRD_001016 C3 C3 C 0 1 N N N 56.322 -134.045 34.834 4.258 -1.113 0.027 MH9 1 C2 polymer 1 1 4 ? ? ? PRD_001016 C4 C4 C 0 1 N N N 55.317 -133.365 33.995 5.513 -0.822 -0.666 MH9 1 C3 polymer 1 1 5 ? ? ? PRD_001016 C5 C5 C 0 1 N N N 53.980 -133.427 34.148 6.655 -1.357 -0.231 MH9 1 C4 polymer 1 1 6 ? ? ? PRD_001016 C6 C6 C 0 1 N N N 53.096 -132.693 33.160 7.948 -1.058 -0.945 MH9 1 C5 polymer 1 1 7 ? ? ? PRD_001016 C7 C7 C 0 1 N N N 51.612 -133.130 33.193 8.964 -0.499 0.053 MH9 1 C6 polymer 1 1 8 ? ? ? PRD_001016 C8 C8 C 0 1 N N N 50.825 -132.358 32.092 10.277 -0.195 -0.672 MH9 1 C7 polymer 1 1 9 ? ? ? PRD_001016 C9 C9 C 0 1 N N N 49.315 -132.731 32.029 11.293 0.364 0.326 MH9 1 C8 polymer 1 1 10 ? ? ? PRD_001016 C10 C10 C 0 1 N N N 48.632 -131.954 30.858 12.606 0.668 -0.399 MH9 1 C9 polymer 1 1 11 ? ? ? PRD_001016 C11 C11 C 0 1 N N N 47.111 -132.263 30.670 13.622 1.226 0.599 MH9 1 C10 polymer 1 1 12 ? ? ? PRD_001016 C12 C12 C 0 1 N N N 46.546 -131.459 29.454 14.935 1.531 -0.126 MH9 1 C11 polymer 1 1 13 ? ? ? PRD_001016 N1 N1 N 0 1 N N N 60.059 -134.329 35.035 0.692 -0.326 -0.164 THR 2 N polymer 1 1 14 ? ? ? PRD_001016 C13 C13 C 0 1 N N S 61.247 -134.928 35.718 -0.566 -0.622 0.526 THR 2 CA polymer 1 1 15 ? ? ? PRD_001016 C14 C14 C 0 1 N N N 61.056 -134.968 37.251 -1.717 -0.457 -0.433 THR 2 C polymer 1 1 16 ? ? ? PRD_001016 O2 O2 O 0 1 N N N 60.698 -133.948 37.851 -1.597 0.255 -1.408 THR 2 O polymer 1 1 17 ? ? ? PRD_001016 C15 C15 C 0 1 N N R 62.591 -134.198 35.394 -0.741 0.341 1.702 THR 2 CB polymer 1 1 18 ? ? ? PRD_001016 O3 O3 O 0 1 N N N 62.531 -132.893 35.955 -0.758 1.686 1.219 THR 2 OG1 polymer 1 1 19 ? ? ? PRD_001016 C16 C16 C 0 1 N N N 62.842 -134.092 33.874 0.421 0.166 2.682 THR 2 CG2 polymer 1 1 20 ? ? ? PRD_001016 N2 N2 N 0 1 N N N 61.271 -136.160 37.855 -2.879 -1.101 -0.208 LYO 3 N polymer 1 1 21 ? ? ? PRD_001016 C17 C17 C 0 1 N N S 61.099 -136.357 39.288 -3.955 -1.033 -1.194 LYO 3 CA polymer 1 1 22 ? ? ? PRD_001016 C18 C18 C 0 1 N N N 62.389 -136.201 40.060 -4.793 0.203 -0.998 LYO 3 C polymer 1 1 23 ? ? ? PRD_001016 O4 O4 O 0 1 N N N 63.470 -136.318 39.469 -5.767 0.370 -1.709 LYO 3 O polymer 1 1 24 ? ? ? PRD_001016 C19 C19 C 0 1 N N N 60.571 -137.796 39.583 -4.818 -2.288 -1.140 LYO 3 CB polymer 1 1 25 ? ? ? PRD_001016 C20 C20 C 0 1 N N S 59.327 -137.844 40.505 -5.654 -2.376 0.130 LYO 3 CG polymer 1 1 26 ? ? ? PRD_001016 O5 O5 O 0 1 N N N 58.286 -137.123 39.827 -5.343 -1.330 1.038 LYO 3 OG polymer 1 1 27 ? ? ? PRD_001016 C21 C21 C 0 1 N N N 58.888 -139.306 40.809 -7.141 -2.361 -0.226 LYO 3 CD polymer 1 1 28 ? ? ? PRD_001016 C22 C22 C 0 1 N N N 59.591 -139.934 42.066 -7.885 -1.293 0.572 LYO 3 CE polymer 1 1 29 ? ? ? PRD_001016 N3 N3 N 0 1 N N N 60.964 -139.457 42.249 -7.807 -0.015 -0.168 LYO 3 NZ polymer 1 1 30 ? ? ? PRD_001016 N4 N4 N 0 1 N N N 62.250 -135.963 41.396 -4.455 1.074 0.000 0W6 4 N polymer 1 1 31 ? ? ? PRD_001016 C23 C23 C 0 1 N N S 63.381 -135.822 42.296 -4.567 2.522 -0.292 0W6 4 CA polymer 1 1 32 ? ? ? PRD_001016 C24 C24 C 0 1 N N N 63.542 -134.333 42.656 -4.427 2.830 -1.777 0W6 4 C16 polymer 1 1 33 ? ? ? PRD_001016 C25 C25 C 0 1 N N N 63.148 -136.707 43.572 -5.863 3.083 0.278 0W6 4 C17 polymer 1 1 34 ? ? ? PRD_001016 C26 C26 C 0 1 N N N 62.822 -138.198 43.247 -7.090 2.344 -0.241 0W6 4 C18 polymer 1 1 35 ? ? ? PRD_001016 C27 C27 C 0 1 N N N 61.358 -138.589 43.248 -7.272 1.045 0.504 0W6 4 C polymer 1 1 36 ? ? ? PRD_001016 O6 O6 O 0 1 N N N 60.599 -138.121 44.108 -6.957 0.950 1.668 0W6 4 O polymer 1 1 37 ? ? ? PRD_001016 H1 H1 H 0 1 N N N 57.944 -133.257 33.794 3.103 0.077 -1.278 MH9 1 H1 polymer 1 1 38 ? ? ? PRD_001016 H2 H2 H 0 1 N N N 55.992 -134.668 35.652 4.256 -1.761 0.891 MH9 1 H2 polymer 1 1 39 ? ? ? PRD_001016 H3 H3 H 0 1 N N N 55.688 -132.760 33.181 5.515 -0.174 -1.531 MH9 1 H3 polymer 1 1 40 ? ? ? PRD_001016 H4 H4 H 0 1 N N N 53.546 -133.990 34.961 6.653 -2.005 0.633 MH9 1 H4 polymer 1 1 41 ? ? ? PRD_001016 H5 H5 H 0 1 N N N 53.144 -131.618 33.386 8.339 -1.974 -1.388 MH9 1 H51 polymer 1 1 42 ? ? ? PRD_001016 H6 H6 H 0 1 N N N 53.486 -132.873 32.147 7.768 -0.323 -1.730 MH9 1 H52 polymer 1 1 43 ? ? ? PRD_001016 H7 H7 H 0 1 N N N 51.543 -134.212 33.004 8.573 0.417 0.496 MH9 1 H61 polymer 1 1 44 ? ? ? PRD_001016 H8 H8 H 0 1 N N N 51.183 -132.902 34.180 9.144 -1.234 0.838 MH9 1 H62 polymer 1 1 45 ? ? ? PRD_001016 H9 H9 H 0 1 N N N 50.909 -131.280 32.295 10.668 -1.111 -1.115 MH9 1 H71 polymer 1 1 46 ? ? ? PRD_001016 H10 H10 H 0 1 N N N 51.280 -132.584 31.116 10.097 0.540 -1.457 MH9 1 H72 polymer 1 1 47 ? ? ? PRD_001016 H11 H11 H 0 1 N N N 49.212 -133.813 31.860 10.902 1.280 0.769 MH9 1 H81 polymer 1 1 48 ? ? ? PRD_001016 H12 H12 H 0 1 N N N 48.831 -132.461 32.979 11.473 -0.371 1.111 MH9 1 H82 polymer 1 1 49 ? ? ? PRD_001016 H13 H13 H 0 1 N N N 48.742 -130.877 31.051 12.997 -0.248 -0.842 MH9 1 H91 polymer 1 1 50 ? ? ? PRD_001016 H14 H14 H 0 1 N N N 49.153 -132.214 29.924 12.426 1.403 -1.184 MH9 1 H92 polymer 1 1 51 ? ? ? PRD_001016 H15 H15 H 0 0 N N N 46.978 -133.340 30.488 13.231 2.142 1.042 MH9 1 H101 polymer 1 1 52 ? ? ? PRD_001016 H16 H16 H 0 0 N N N 46.566 -131.975 31.581 13.802 0.492 1.384 MH9 1 H102 polymer 1 1 53 ? ? ? PRD_001016 H17 H17 H 0 0 N N N 45.476 -131.683 29.331 15.659 1.929 0.585 MH9 1 H111 polymer 1 1 54 ? ? ? PRD_001016 H18 H18 H 0 0 N N N 46.676 -130.382 29.635 15.326 0.615 -0.569 MH9 1 H112 polymer 1 1 55 ? ? ? PRD_001016 H19 H19 H 0 0 N N N 47.088 -131.746 28.541 14.754 2.265 -0.911 MH9 1 H113 polymer 1 1 56 ? ? ? PRD_001016 H20 H20 H 0 1 N N N 60.232 -133.701 34.277 0.693 0.256 -0.940 THR 2 H polymer 1 1 57 ? ? ? PRD_001016 H21 H21 H 0 1 N N N 61.350 -135.967 35.372 -0.545 -1.647 0.896 THR 2 HA polymer 1 1 58 ? ? ? PRD_001016 H22 H22 H 0 1 N N N 63.414 -134.770 35.847 -1.681 0.126 2.211 THR 2 HB polymer 1 1 59 ? ? ? PRD_001016 H23 H23 H 0 1 N N N 61.937 -132.894 36.696 -1.471 1.869 0.592 THR 2 HG1 polymer 1 1 60 ? ? ? PRD_001016 H24 H24 H 0 0 N N N 63.795 -133.573 33.695 1.350 0.477 2.203 THR 2 HG21 polymer 1 1 61 ? ? ? PRD_001016 H25 H25 H 0 0 N N N 62.886 -135.101 33.439 0.246 0.778 3.567 THR 2 HG22 polymer 1 1 62 ? ? ? PRD_001016 H26 H26 H 0 0 N N N 62.023 -133.526 33.406 0.496 -0.882 2.974 THR 2 HG23 polymer 1 1 63 ? ? ? PRD_001016 H27 H27 H 0 1 N N N 61.560 -136.937 37.295 -3.001 -1.610 0.609 LYO 3 H2 polymer 1 1 64 ? ? ? PRD_001016 H28 H28 H 0 1 N N N 60.364 -135.635 39.674 -3.498 -0.974 -2.196 LYO 3 HA polymer 1 1 65 ? ? ? PRD_001016 H29 H29 H 0 1 N N N 60.308 -138.269 38.625 -5.477 -2.312 -2.015 LYO 3 HB1 polymer 1 1 66 ? ? ? PRD_001016 H30 H30 H 0 1 N N N 61.379 -138.367 40.065 -4.164 -3.169 -1.198 LYO 3 HB2 polymer 1 1 67 ? ? ? PRD_001016 H31 H31 H 0 1 N N N 59.574 -137.348 41.455 -5.433 -3.338 0.622 LYO 3 HG polymer 1 1 68 ? ? ? PRD_001016 H32 H32 H 0 1 N N N 57.499 -137.127 40.359 -5.766 -1.421 1.902 LYO 3 HOG polymer 1 1 69 ? ? ? PRD_001016 H33 H33 H 0 1 N N N 57.801 -139.313 40.981 -7.255 -2.157 -1.294 LYO 3 HD1 polymer 1 1 70 ? ? ? PRD_001016 H34 H34 H 0 1 N N N 59.125 -139.928 39.933 -7.574 -3.342 -0.013 LYO 3 HD2 polymer 1 1 71 ? ? ? PRD_001016 H35 H35 H 0 1 N N N 59.007 -139.674 42.961 -8.939 -1.589 0.662 LYO 3 HE1 polymer 1 1 72 ? ? ? PRD_001016 H36 H36 H 0 1 N N N 59.612 -141.027 41.947 -7.470 -1.193 1.570 LYO 3 HE2 polymer 1 1 73 ? ? ? PRD_001016 H37 H37 H 0 1 N N N 61.661 -139.781 41.609 -8.125 0.072 -1.082 LYO 3 HZ2 polymer 1 1 74 ? ? ? PRD_001016 H38 H38 H 0 1 N N N 61.327 -135.882 41.773 -4.111 0.776 0.867 0W6 4 H polymer 1 1 75 ? ? ? PRD_001016 H39 H39 H 0 1 N N N 64.300 -136.166 41.799 -3.727 3.027 0.228 0W6 4 HA polymer 1 1 76 ? ? ? PRD_001016 H40 H40 H 0 1 N N N 63.703 -133.749 41.738 -5.212 2.315 -2.330 0W6 4 H12 polymer 1 1 77 ? ? ? PRD_001016 H41 H41 H 0 1 N N N 62.632 -133.978 43.162 -4.516 3.905 -1.935 0W6 4 H13 polymer 1 1 78 ? ? ? PRD_001016 H42 H42 H 0 1 N N N 64.406 -134.209 43.325 -3.452 2.491 -2.128 0W6 4 H14 polymer 1 1 79 ? ? ? PRD_001016 H43 H43 H 0 1 N N N 62.307 -136.283 44.140 -5.829 3.007 1.369 0W6 4 H15 polymer 1 1 80 ? ? ? PRD_001016 H44 H44 H 0 1 N N N 64.059 -136.676 44.188 -5.939 4.144 0.022 0W6 4 H16 polymer 1 1 81 ? ? ? PRD_001016 H45 H45 H 0 1 N N N 63.225 -138.417 42.247 -7.977 2.965 -0.078 0W6 4 H17 polymer 1 1 82 ? ? ? PRD_001016 H46 H46 H 0 1 N N N 63.334 -138.822 43.994 -7.002 2.148 -1.306 0W6 4 H18 polymer 1 1 83 ? ? ? # 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 PRD_001016 C1 O1 DOUB N N 1 PRD_001016 C1 C2 SING N N 2 PRD_001016 C2 C3 DOUB N N 3 PRD_001016 C3 C4 SING N E 4 PRD_001016 C4 C5 DOUB N N 5 PRD_001016 C5 C6 SING N N 6 PRD_001016 C6 C7 SING N N 7 PRD_001016 C7 C8 SING N E 8 PRD_001016 C8 C9 SING N N 9 PRD_001016 C9 C10 SING N N 10 PRD_001016 C10 C11 SING N N 11 PRD_001016 C11 C12 SING N N 12 PRD_001016 C2 H1 SING N N 13 PRD_001016 C3 H2 SING N N 14 PRD_001016 C4 H3 SING N N 15 PRD_001016 C5 H4 SING N N 16 PRD_001016 C6 H5 SING N N 17 PRD_001016 C6 H6 SING N N 18 PRD_001016 C7 H7 SING N N 19 PRD_001016 C7 H8 SING N N 20 PRD_001016 C8 H9 SING N N 21 PRD_001016 C8 H10 SING N N 22 PRD_001016 C9 H11 SING N N 23 PRD_001016 C9 H12 SING N N 24 PRD_001016 C10 H13 SING N N 25 PRD_001016 C10 H14 SING N N 26 PRD_001016 C11 H15 SING N N 27 PRD_001016 C11 H16 SING N N 28 PRD_001016 C12 H17 SING N N 29 PRD_001016 C12 H18 SING N N 30 PRD_001016 C12 H19 SING N N 31 PRD_001016 N1 C13 SING N N 32 PRD_001016 N1 H20 SING N N 33 PRD_001016 C13 C14 SING N N 34 PRD_001016 C13 C15 SING N N 35 PRD_001016 C13 H21 SING N N 36 PRD_001016 C14 O2 DOUB N N 37 PRD_001016 C15 O3 SING N N 38 PRD_001016 C15 C16 SING N N 39 PRD_001016 C15 H22 SING N N 40 PRD_001016 O3 H23 SING N N 41 PRD_001016 C16 H24 SING N N 42 PRD_001016 C16 H25 SING N N 43 PRD_001016 C16 H26 SING N N 44 PRD_001016 N2 C17 SING N N 45 PRD_001016 C17 C18 SING N N 46 PRD_001016 C17 C19 SING N N 47 PRD_001016 C18 O4 DOUB N N 48 PRD_001016 C19 C20 SING N N 49 PRD_001016 C20 O5 SING N N 50 PRD_001016 C20 C21 SING N N 51 PRD_001016 C21 C22 SING N N 52 PRD_001016 C22 N3 SING N N 53 PRD_001016 N2 H27 SING N N 54 PRD_001016 C17 H28 SING N N 55 PRD_001016 C19 H29 SING N N 56 PRD_001016 C19 H30 SING N N 57 PRD_001016 C20 H31 SING N N 58 PRD_001016 O5 H32 SING N N 59 PRD_001016 C21 H33 SING N N 60 PRD_001016 C21 H34 SING N N 61 PRD_001016 C22 H35 SING N N 62 PRD_001016 C22 H36 SING N N 63 PRD_001016 N3 H37 SING N N 64 PRD_001016 C25 C26 SING N N 65 PRD_001016 C25 C23 SING N N 66 PRD_001016 C24 C23 SING N N 67 PRD_001016 O6 C27 DOUB N N 68 PRD_001016 C26 C27 SING N N 69 PRD_001016 C23 N4 SING N N 70 PRD_001016 N4 H38 SING N N 71 PRD_001016 C23 H39 SING N N 72 PRD_001016 C24 H40 SING N N 73 PRD_001016 C24 H41 SING N N 74 PRD_001016 C24 H42 SING N N 75 PRD_001016 C25 H43 SING N N 76 PRD_001016 C25 H44 SING N N 77 PRD_001016 C26 H45 SING N N 78 PRD_001016 C26 H46 SING N N 79 PRD_001016 C1 N1 SING N N 80 PRD_001016 C14 N2 SING N N 81 PRD_001016 C18 N4 SING N N 82 PRD_001016 N3 C27 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 PRD_001016 SMILES ACDLabs 12.01 "O=C(\C=C\C=C/CCCCCCC)NC(C(=O)NC1C(=O)NC(CCC(=O)NCCC(O)C1)C)C(O)C" PRD_001016 InChI InChI 1.03 "InChI=1S/C27H46N4O6/c1-4-5-6-7-8-9-10-11-12-13-24(35)31-25(20(3)32)27(37)30-22-18-21(33)16-17-28-23(34)15-14-19(2)29-26(22)36/h10-13,19-22,25,32-33H,4-9,14-18H2,1-3H3,(H,28,34)(H,29,36)(H,30,37)(H,31,35)" PRD_001016 InChIKey InChI 1.03 MCYAPDZYLYAJFS-UHFFFAOYSA-N PRD_001016 SMILES_CANONICAL CACTVS 3.370 "CCCCCCC/C=C/C=C/C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@H]1C[C@@H](O)CCNC(=O)CC[C@H](C)NC1=O" PRD_001016 SMILES CACTVS 3.370 "CCCCCCCC=CC=CC(=O)N[CH]([CH](C)O)C(=O)N[CH]1C[CH](O)CCNC(=O)CC[CH](C)NC1=O" PRD_001016 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCCC/C=C/C=C/C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@H]1C[C@H](CCNC(=O)CC[C@@H](NC1=O)C)O" PRD_001016 SMILES "OpenEye OEToolkits" 1.7.6 "CCCCCCCC=CC=CC(=O)NC(C(C)O)C(=O)NC1CC(CCNC(=O)CCC(NC1=O)C)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 PRD_001016 "SYSTEMATIC NAME" ACDLabs 12.01 "(2E,4E)-N-[(2R,3S)-3-hydroxy-1-{[(5R,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododecan-8-yl]amino}-1-oxobutan-2-yl]dodeca-2,4-dienamide" PRD_001016 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E,4E)-N-[(2S,3R)-1-[[(5S,8S,10S)-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]dodeca-2,4-dienamide" #