data_3YI # _chem_comp.id 3YI _chem_comp.name ;(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C38 H47 N O13" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "3-formyl rifamycin SV" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-26 _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 725.779 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3YI _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 6BEF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 3YI C1 C1 C 0 1 Y N N 91.471 103.003 42.197 -4.944 -0.139 0.126 C1 3YI 1 3YI N1 N1 N 0 1 N N N 92.116 100.736 42.450 -4.948 2.318 0.262 N1 3YI 2 3YI O1 O1 O 0 1 N N N 90.771 102.548 41.077 -6.301 -0.186 0.064 O1 3YI 3 3YI C2 C2 C 0 1 Y N N 92.163 102.076 42.948 -4.299 1.072 0.259 C2 3YI 4 3YI O2 O2 O 0 1 N N N 90.046 104.947 40.580 -6.171 -2.666 -0.067 O2 3YI 5 3YI C3 C3 C 0 1 Y N N 92.890 102.477 44.078 -2.882 1.109 0.411 C3 3YI 6 3YI O3 O3 O 0 1 N N N 91.655 108.429 43.321 -1.796 -4.775 -0.241 O3 3YI 7 3YI C4 C4 C 0 1 Y N N 92.891 103.854 44.418 -2.131 -0.063 0.335 C4 3YI 8 3YI O4 O4 O 0 1 N N N 93.456 106.787 45.829 0.294 -1.953 -0.111 O4 3YI 9 3YI C5 C5 C 0 1 Y N N 92.186 106.268 43.883 -2.004 -2.519 -0.087 C5 3YI 10 3YI O5 O5 O 0 1 N N N 93.875 109.233 44.143 0.526 -4.826 0.253 O5 3YI 11 3YI C6 C6 C 0 1 Y N N 91.524 107.112 43.009 -2.678 -3.745 -0.158 C6 3YI 12 3YI O6 O6 O 0 1 N N N 94.955 107.859 39.609 3.287 -2.144 1.419 O6 3YI 13 3YI C7 C7 C 0 1 Y N N 90.802 106.670 41.917 -4.076 -3.749 -0.152 C7 3YI 14 3YI O7 O7 O 0 1 N N N 97.615 106.005 40.687 5.781 -0.609 -0.044 O7 3YI 15 3YI C8 C8 C 0 1 Y N N 90.761 105.331 41.668 -4.818 -2.593 -0.054 C8 3YI 16 3YI O8 O8 O 0 1 N N N 97.942 106.195 38.444 5.436 -0.022 2.059 O8 3YI 17 3YI C9 C9 C 0 1 Y N N 91.462 104.387 42.494 -4.189 -1.332 0.061 C9 3YI 18 3YI O9 O9 O 0 1 N N N 96.926 103.341 38.486 3.456 1.748 0.819 O9 3YI 19 3YI C10 C10 C 0 1 Y N N 92.191 104.844 43.631 -2.774 -1.285 0.103 C10 3YI 20 3YI O10 O10 O 0 1 N N N 95.399 101.052 39.146 2.491 4.800 0.270 O10 3YI 21 3YI C11 C11 C 0 1 N N N 92.777 107.103 44.879 -0.610 -2.756 -0.223 C11 3YI 22 3YI O11 O11 O 0 1 N N N 91.146 99.780 44.224 -3.608 3.278 -1.098 O11 3YI 23 3YI C12 C12 C 0 1 N N S 92.567 108.545 44.488 -0.503 -4.242 -0.543 C12 3YI 24 3YI O12 O12 O 0 1 N N N 93.614 104.222 45.515 -0.784 -0.021 0.484 O12 3YI 25 3YI C13 C13 C 0 1 N N N 91.848 109.388 45.530 -0.207 -4.427 -2.033 C13 3YI 26 3YI O13 O13 O 0 1 N N N 94.869 101.288 44.854 -1.006 2.474 0.522 O13 3YI 27 3YI C14 C14 C 0 1 N N N 90.087 107.667 41.029 -4.798 -5.068 -0.257 C14 3YI 28 3YI C15 C15 C 0 1 N N N 91.631 99.696 43.127 -4.139 3.340 -0.005 C15 3YI 29 3YI C16 C16 C 0 1 N N N 91.760 98.401 42.425 -3.776 4.500 0.754 C16 3YI 30 3YI C17 C17 C 0 1 N N N 92.865 98.116 41.689 -2.495 4.960 0.660 C17 3YI 31 3YI C18 C18 C 0 1 N N N 94.016 98.964 41.563 -1.542 4.232 -0.179 C18 3YI 32 3YI C19 C19 C 0 1 N N N 95.053 98.598 40.791 -0.240 4.523 -0.140 C19 3YI 33 3YI C20 C20 C 0 1 N N S 96.409 99.336 40.593 0.726 3.759 -1.009 C20 3YI 34 3YI C21 C21 C 0 1 N N S 96.212 100.855 40.299 2.043 3.550 -0.259 C21 3YI 35 3YI C22 C22 C 0 1 N N R 97.536 101.666 40.133 3.097 2.995 -1.219 C22 3YI 36 3YI C23 C23 C 0 1 N N R 97.352 103.165 39.840 4.014 2.030 -0.466 C23 3YI 37 3YI C24 C24 C 0 1 N N R 96.402 103.914 40.798 4.149 0.729 -1.260 C24 3YI 38 3YI C25 C25 C 0 1 N N S 96.321 105.415 40.451 4.361 -0.438 -0.293 C25 3YI 39 3YI C26 C26 C 0 1 N N R 95.347 106.221 41.327 3.794 -1.720 -0.909 C26 3YI 40 3YI C27 C27 C 0 1 N N S 95.336 107.749 40.995 3.623 -2.780 0.184 C27 3YI 41 3YI C28 C28 C 0 1 N N N 94.404 108.547 41.897 2.516 -3.725 -0.213 C28 3YI 42 3YI C29 C29 C 0 1 N N N 94.801 108.486 43.343 1.537 -3.994 0.624 C29 3YI 43 3YI C30 C30 C 0 1 N N N 90.589 97.467 42.557 -4.736 5.201 1.676 C30 3YI 44 3YI C31 C31 C 0 1 N N N 97.292 99.153 41.833 0.123 2.398 -1.366 C31 3YI 45 3YI C32 C32 C 0 1 N N N 98.473 101.018 39.071 3.927 4.148 -1.786 C32 3YI 46 3YI C33 C33 C 0 1 N N N 96.874 103.698 42.252 5.346 0.831 -2.207 C33 3YI 47 3YI C34 C34 C 0 1 N N N 93.955 105.639 41.171 2.436 -1.421 -1.546 C34 3YI 48 3YI C35 C35 C 0 1 N N N 98.351 106.362 39.610 6.222 -0.322 1.192 C35 3YI 49 3YI C36 C36 C 0 1 N N N 99.677 106.965 39.999 7.697 -0.376 1.497 C36 3YI 50 3YI C37 C37 C 0 1 N N N 95.879 108.602 38.840 3.813 -2.802 2.573 C37 3YI 51 3YI C38 C38 C 0 1 N N N 93.643 101.514 44.882 -2.209 2.388 0.649 C38 3YI 52 3YI H1 H1 H 0 1 N N N 92.472 100.568 41.531 -5.896 2.423 0.440 H1 3YI 53 3YI H2 H2 H 0 1 N N N 90.866 101.606 41.005 -6.732 -0.272 0.926 H2 3YI 54 3YI H3 H3 H 0 1 N N N 90.080 104.001 40.496 -6.569 -2.764 0.809 H3 3YI 55 3YI H4 H4 H 0 1 N N N 96.813 104.267 38.307 3.343 2.528 1.378 H4 3YI 56 3YI H5 H5 H 0 1 N N N 94.591 100.561 39.240 1.872 5.210 0.889 H5 3YI 57 3YI H6 H6 H 0 1 N N N 93.557 105.163 45.631 -0.486 -0.124 1.398 H6 3YI 58 3YI H7 H7 H 0 1 N N N 92.489 109.501 46.417 -0.975 -3.925 -2.621 H7 3YI 59 3YI H8 H8 H 0 1 N N N 91.626 110.380 45.109 0.767 -3.997 -2.267 H8 3YI 60 3YI H9 H9 H 0 1 N N N 90.909 108.893 45.817 -0.202 -5.490 -2.274 H9 3YI 61 3YI H10 H10 H 0 1 N N N 89.066 107.827 41.405 -4.967 -5.470 0.742 H10 3YI 62 3YI H11 H11 H 0 1 N N N 90.634 108.622 41.035 -5.755 -4.919 -0.755 H11 3YI 63 3YI H12 H12 H 0 1 N N N 90.043 107.277 40.002 -4.193 -5.768 -0.832 H12 3YI 64 3YI H13 H13 H 0 1 N N N 92.879 97.177 41.156 -2.193 5.831 1.212 H13 3YI 65 3YI H14 H14 H 0 1 N N N 94.049 99.904 42.093 -1.889 3.436 -0.823 H14 3YI 66 3YI H15 H15 H 0 1 N N N 94.930 97.678 40.239 0.121 5.302 0.513 H15 3YI 67 3YI H16 H16 H 0 1 N N N 96.922 98.885 39.731 0.915 4.322 -1.923 H16 3YI 68 3YI H17 H17 H 0 1 N N N 95.688 101.280 41.168 1.888 2.845 0.557 H17 3YI 69 3YI H18 H18 H 0 1 N N N 98.064 101.597 41.096 2.604 2.467 -2.034 H18 3YI 70 3YI H19 H19 H 0 1 N N N 98.342 103.632 39.949 4.997 2.484 -0.344 H19 3YI 71 3YI H20 H20 H 0 1 N N N 95.396 103.481 40.694 3.241 0.561 -1.839 H20 3YI 72 3YI H21 H21 H 0 1 N N N 96.034 105.526 39.395 3.850 -0.229 0.647 H21 3YI 73 3YI H22 H22 H 0 1 N N N 95.656 106.107 42.377 4.479 -2.091 -1.671 H22 3YI 74 3YI H23 H23 H 0 1 N N N 96.359 108.132 41.126 4.553 -3.336 0.301 H23 3YI 75 3YI H24 H24 H 0 1 N N N 93.549 109.098 41.535 2.536 -4.190 -1.190 H24 3YI 76 3YI H26 H26 H 0 1 N N N 95.660 107.956 43.726 1.537 -3.553 1.610 H26 3YI 77 3YI H28 H28 H 0 1 N N N 89.825 97.925 43.203 -4.663 4.768 2.674 H28 3YI 78 3YI H29 H29 H 0 1 N N N 90.160 97.274 41.563 -4.488 6.261 1.721 H29 3YI 79 3YI H30 H30 H 0 1 N N N 90.925 96.519 43.002 -5.753 5.081 1.302 H30 3YI 80 3YI H31 H31 H 0 1 N N N 97.426 98.080 42.033 -0.919 2.528 -1.657 H31 3YI 81 3YI H32 H32 H 0 1 N N N 98.273 99.618 41.656 0.680 1.960 -2.194 H32 3YI 82 3YI H33 H33 H 0 1 N N N 96.811 99.630 42.699 0.179 1.738 -0.500 H33 3YI 83 3YI H34 H34 H 0 1 N N N 98.595 99.948 39.293 4.420 4.677 -0.971 H34 3YI 84 3YI H35 H35 H 0 1 N N N 98.031 101.137 38.071 4.679 3.753 -2.470 H35 3YI 85 3YI H36 H36 H 0 1 N N N 99.455 101.512 39.098 3.274 4.836 -2.323 H36 3YI 86 3YI H37 H37 H 0 1 N N N 96.200 104.230 42.940 6.254 0.999 -1.627 H37 3YI 87 3YI H38 H38 H 0 1 N N N 96.862 102.623 42.485 5.443 -0.096 -2.772 H38 3YI 88 3YI H39 H39 H 0 1 N N N 97.897 104.087 42.367 5.195 1.662 -2.895 H39 3YI 89 3YI H40 H40 H 0 1 N N N 93.248 106.207 41.793 2.583 -0.869 -2.475 H40 3YI 90 3YI H41 H41 H 0 1 N N N 93.648 105.701 40.117 1.920 -2.357 -1.758 H41 3YI 91 3YI H42 H42 H 0 1 N N N 93.960 104.586 41.490 1.836 -0.823 -0.860 H42 3YI 92 3YI H43 H43 H 0 1 N N N 100.236 107.239 39.092 7.861 -0.115 2.542 H43 3YI 93 3YI H44 H44 H 0 1 N N N 99.506 107.864 40.609 8.070 -1.383 1.311 H44 3YI 94 3YI H45 H45 H 0 1 N N N 100.257 106.232 40.580 8.226 0.332 0.858 H45 3YI 95 3YI H46 H46 H 0 1 N N N 95.534 108.650 37.797 3.444 -2.309 3.472 H46 3YI 96 3YI H47 H47 H 0 1 N N N 95.959 109.621 39.247 3.495 -3.845 2.574 H47 3YI 97 3YI H48 H48 H 0 1 N N N 96.864 108.114 38.878 4.902 -2.754 2.553 H48 3YI 98 3YI H49 H49 H 0 1 N N N 93.068 100.929 45.584 -2.785 3.256 0.937 H49 3YI 99 # # 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 3YI O8 C35 DOUB N N 1 3YI O9 C23 SING N N 2 3YI C37 O6 SING N N 3 3YI C32 C22 SING N N 4 3YI O10 C21 SING N N 5 3YI O6 C27 SING N N 6 3YI C35 C36 SING N N 7 3YI C35 O7 SING N N 8 3YI C23 C22 SING N N 9 3YI C23 C24 SING N N 10 3YI C22 C21 SING N N 11 3YI C21 C20 SING N N 12 3YI C25 O7 SING N N 13 3YI C25 C24 SING N N 14 3YI C25 C26 SING N N 15 3YI O2 C8 SING N N 16 3YI C20 C19 SING N N 17 3YI C20 C31 SING N N 18 3YI C19 C18 DOUB N E 19 3YI C24 C33 SING N N 20 3YI C27 C26 SING N N 21 3YI C27 C28 SING N N 22 3YI C14 C7 SING N N 23 3YI O1 C1 SING N N 24 3YI C34 C26 SING N N 25 3YI C18 C17 SING N N 26 3YI C8 C7 DOUB Y N 27 3YI C8 C9 SING Y N 28 3YI C17 C16 DOUB N Z 29 3YI C28 C29 DOUB N E 30 3YI C7 C6 SING Y N 31 3YI C1 C9 DOUB Y N 32 3YI C1 C2 SING Y N 33 3YI C16 C30 SING N N 34 3YI C16 C15 SING N N 35 3YI N1 C2 SING N N 36 3YI N1 C15 SING N N 37 3YI C9 C10 SING Y N 38 3YI C2 C3 DOUB Y N 39 3YI C6 O3 SING N N 40 3YI C6 C5 DOUB Y N 41 3YI C15 O11 DOUB N N 42 3YI O3 C12 SING N N 43 3YI C29 O5 SING N N 44 3YI C10 C5 SING Y N 45 3YI C10 C4 DOUB Y N 46 3YI C5 C11 SING N N 47 3YI C3 C4 SING Y N 48 3YI C3 C38 SING N N 49 3YI O5 C12 SING N N 50 3YI C4 O12 SING N N 51 3YI C12 C11 SING N N 52 3YI C12 C13 SING N N 53 3YI O13 C38 DOUB N N 54 3YI C11 O4 DOUB N N 55 3YI N1 H1 SING N N 56 3YI O1 H2 SING N N 57 3YI O2 H3 SING N N 58 3YI O9 H4 SING N N 59 3YI O10 H5 SING N N 60 3YI O12 H6 SING N N 61 3YI C13 H7 SING N N 62 3YI C13 H8 SING N N 63 3YI C13 H9 SING N N 64 3YI C14 H10 SING N N 65 3YI C14 H11 SING N N 66 3YI C14 H12 SING N N 67 3YI C17 H13 SING N N 68 3YI C18 H14 SING N N 69 3YI C19 H15 SING N N 70 3YI C20 H16 SING N N 71 3YI C21 H17 SING N N 72 3YI C22 H18 SING N N 73 3YI C23 H19 SING N N 74 3YI C24 H20 SING N N 75 3YI C25 H21 SING N N 76 3YI C26 H22 SING N N 77 3YI C27 H23 SING N N 78 3YI C28 H24 SING N N 79 3YI C29 H26 SING N N 80 3YI C30 H28 SING N N 81 3YI C30 H29 SING N N 82 3YI C30 H30 SING N N 83 3YI C31 H31 SING N N 84 3YI C31 H32 SING N N 85 3YI C31 H33 SING N N 86 3YI C32 H34 SING N N 87 3YI C32 H35 SING N N 88 3YI C32 H36 SING N N 89 3YI C33 H37 SING N N 90 3YI C33 H38 SING N N 91 3YI C33 H39 SING N N 92 3YI C34 H40 SING N N 93 3YI C34 H41 SING N N 94 3YI C34 H42 SING N N 95 3YI C36 H43 SING N N 96 3YI C36 H44 SING N N 97 3YI C36 H45 SING N N 98 3YI C37 H46 SING N N 99 3YI C37 H47 SING N N 100 3YI C37 H48 SING N N 101 3YI C38 H49 SING N N 102 # # 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 3YI SMILES ACDLabs 12.01 "c1(c4c(O)c(c3OC2(OC=CC(OC)C(C(OC(=O)C)C(C(O)C(C(O)C(C=CC=C(C(Nc1c(c(O)c4c3C2=O)C=O)=O)C)C)C)C)C)C)C)O" 3YI InChI InChI 1.03 "InChI=1S/C38H47NO13/c1-16-11-10-12-17(2)37(48)39-28-23(15-40)32(45)25-26(33(28)46)31(44)21(6)35-27(25)36(47)38(8,52-35)50-14-13-24(49-9)18(3)34(51-22(7)41)20(5)30(43)19(4)29(16)42/h10-16,18-20,24,29-30,34,42-46H,1-9H3,(H,39,48)/b11-10+,14-13+,17-12-/t16-,18+,19+,20+,24-,29-,30+,34+,38-/m0/s1" 3YI InChIKey InChI 1.03 BBNQHOMJRFAQBN-UPZFVJMDSA-N 3YI SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(C=O)c(O)c4c3C2=O" 3YI SMILES CACTVS 3.385 "CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=O)c(O)c4c3C2=O" 3YI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](/C=C/C=C(\C(=O)Nc(c2O)c(c3O)C=O)/C)C)O)C)O)C)OC(=O)C)C)OC)C)O" 3YI SMILES "OpenEye OEToolkits" 2.0.6 "Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=O)C)C)O)C)O)C)OC(=O)C)C)OC)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 3YI "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate" 3YI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(4~{Z},6~{E},8~{S},9~{S},10~{R},11~{R},12~{R},13~{S},14~{R},15~{S},16~{E},19~{S})-24-methanoyl-15-methoxy-4,8,10,12,14,19,28-heptamethyl-9,11,23,25,27-pentakis(oxidanyl)-3,20-bis(oxidanylidene)-18,30-dioxa-2-azatetracyclo[17.6.5.0^{21,29}.0^{22,26}]triaconta-1(24),4,6,16,21(29),22,25,27-octaen-13-yl] ethanoate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3YI "Create component" 2017-10-26 RCSB 3YI "Initial release" 2018-07-18 RCSB 3YI "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3YI _pdbx_chem_comp_synonyms.name "3-formyl rifamycin SV" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##