data_2YD
# 
_chem_comp.id                                    2YD 
_chem_comp.name                                  "(5R,6R,7S,8R,9R,12S,13E,16S,18S,19R,20aR)-4,7,19-trihydroxy-2,6,8,12,14,16,18-heptamethyl-6,7,8,9,10,11,12,15,16,17,18,19,20,20a-tetradecahydro-1,19:5,9-diepoxybenzo[18]annulen-3(5H)-one" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H44 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         Kendomycin 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-05-01 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        488.656 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     2YD 
_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        4Q1S 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
2YD O1  O1  O 0 1 N N N N N N 75.861 -145.584 57.902 4.332  0.723  -0.162 O1  2YD 1  
2YD C1  C1  C 0 1 N N N N N N 75.006 -146.205 58.718 3.454  -0.311 -0.080 C1  2YD 2  
2YD C   C   C 0 1 N N N N N N 73.768 -146.743 58.120 3.976  -1.655 -0.417 C   2YD 3  
2YD O   O   O 0 1 N N N N N N 73.546 -146.483 56.951 5.182  -1.815 -0.466 O   2YD 4  
2YD C2  C2  C 0 1 N N N N N N 75.275 -146.368 60.033 2.166  -0.155 0.275  C2  2YD 5  
2YD C3  C3  C 0 1 N N R N N N 74.459 -147.405 60.796 1.375  -1.431 0.394  C3  2YD 6  
2YD C22 C22 C 0 1 N N R N N N 76.507 -145.785 60.715 1.502  1.158  0.582  C22 2YD 7  
2YD C23 C23 C 0 1 N N R N N N 76.282 -144.627 61.737 2.459  2.299  0.880  C23 2YD 8  
2YD C27 C27 C 0 1 N N N N N N 75.610 -143.368 61.110 3.201  2.013  2.195  C27 2YD 9  
2YD C24 C24 C 0 1 N N S N N N 77.654 -144.336 62.449 1.713  3.627  1.059  C24 2YD 10 
2YD O5  O5  O 0 1 N N N N N N 77.494 -143.329 63.475 2.663  4.697  1.078  O5  2YD 11 
2YD C25 C25 C 0 1 N N R N N N 78.336 -145.622 63.059 0.716  3.859  -0.076 C25 2YD 12 
2YD C26 C26 C 0 1 N N N N N N 77.706 -146.111 64.405 1.467  4.031  -1.399 C26 2YD 13 
2YD O4  O4  O 0 1 N N N N N N 77.095 -146.919 61.392 0.611  1.508  -0.488 O4  2YD 14 
2YD C21 C21 C 0 1 N N R N N N 78.394 -146.743 61.964 -0.204 2.639  -0.155 C21 2YD 15 
2YD C20 C20 C 0 1 N N N N N N 78.752 -148.181 62.450 -1.323 2.842  -1.162 C20 2YD 16 
2YD C19 C19 C 0 1 N N N N N N 78.832 -149.199 61.280 -2.668 2.818  -0.421 C19 2YD 17 
2YD C17 C17 C 0 1 N N S N N N 79.049 -150.681 61.756 -3.739 2.241  -1.342 C17 2YD 18 
2YD C18 C18 C 0 1 N N N N N N 79.369 -151.564 60.508 -5.067 2.972  -1.150 C18 2YD 19 
2YD C16 C16 C 0 1 N N N N N N 77.871 -151.313 62.515 -3.882 0.761  -1.171 C16 2YD 20 
2YD C15 C15 C 0 1 N N N N N N 77.647 -151.545 63.848 -4.279 0.142  -0.095 C15 2YD 21 
2YD C28 C28 C 0 1 N N N N N N 78.635 -151.244 64.964 -4.660 0.847  1.181  C28 2YD 22 
2YD C14 C14 C 0 1 N N N N N N 76.321 -152.109 64.399 -4.377 -1.371 -0.140 C14 2YD 23 
2YD C12 C12 C 0 1 N N S N N N 75.031 -152.022 63.508 -3.411 -1.989 0.877  C12 2YD 24 
2YD C13 C13 C 0 1 N N N N N N 73.852 -152.786 64.178 -4.206 -2.318 2.149  C13 2YD 25 
2YD C11 C11 C 0 1 N N N N N N 74.684 -150.513 63.234 -2.827 -3.281 0.319  C11 2YD 26 
2YD C9  C9  C 0 1 N N S N N N 73.710 -150.175 62.065 -1.337 -3.421 0.585  C9  2YD 27 
2YD C10 C10 C 0 1 N N N N N N 74.332 -150.549 60.687 -0.970 -3.106 2.028  C10 2YD 28 
2YD C5  C5  C 0 1 N N R N N N 73.096 -148.723 62.232 -0.499 -2.642 -0.416 C5  2YD 29 
2YD C4  C4  C 0 1 N N N N N N 74.014 -147.447 62.273 -0.099 -1.230 0.045  C4  2YD 30 
2YD O2  O2  O 0 1 N N N N N N 72.211 -148.734 63.377 -1.214 -2.534 -1.663 O2  2YD 31 
2YD O3  O3  O 0 1 N N N N N N 72.316 -148.377 61.075 0.734  -3.377 -0.683 O3  2YD 32 
2YD C6  C6  C 0 1 N N N N N N 73.118 -147.722 60.208 1.813  -2.647 -0.385 C6  2YD 33 
2YD C7  C7  C 0 1 N N N N N N 72.808 -147.531 58.919 3.122  -2.744 -0.680 C7  2YD 34 
2YD C8  C8  C 0 1 N N N N N N 71.494 -148.020 58.360 3.667  -4.009 -1.284 C8  2YD 35 
2YD H1  H1  H 0 1 N N N N N N 75.494 -145.547 57.027 5.223  0.461  -0.430 H1  2YD 36 
2YD H4  H4  H 0 1 N N N N N N 75.033 -148.335 60.671 1.412  -1.707 1.459  H4  2YD 37 
2YD H5  H5  H 0 1 N N N N N N 77.197 -145.423 59.938 0.873  1.005  1.481  H5  2YD 38 
2YD H6  H6  H 0 1 N N N N N N 75.596 -145.008 62.508 3.182  2.426  0.076  H6  2YD 39 
2YD H7  H7  H 0 1 N N N N N N 75.483 -142.596 61.883 3.761  1.083  2.101  H7  2YD 40 
2YD H8  H8  H 0 1 N N N N N N 76.246 -142.977 60.303 3.888  2.832  2.410  H8  2YD 41 
2YD H9  H9  H 0 1 N N N N N N 74.627 -143.643 60.701 2.479  1.922  3.007  H9  2YD 42 
2YD H10 H10 H 0 1 N N N N N N 78.338 -143.946 61.681 1.176  3.606  2.010  H10 2YD 43 
2YD H11 H11 H 0 1 N N N N N N 78.331 -143.167 63.893 3.314  4.633  1.791  H11 2YD 44 
2YD H12 H12 H 0 1 N N N N N N 79.378 -145.347 63.281 0.123  4.750  0.127  H12 2YD 45 
2YD H13 H13 H 0 1 N N N N N N 77.694 -145.282 65.128 2.046  3.132  -1.608 H13 2YD 46 
2YD H14 H14 H 0 1 N N N N N N 76.677 -146.454 64.225 0.750  4.196  -2.204 H14 2YD 47 
2YD H15 H15 H 0 1 N N N N N N 78.304 -146.941 64.809 2.137  4.887  -1.328 H15 2YD 48 
2YD H16 H16 H 0 1 N N N N N N 79.117 -146.442 61.191 -0.637 2.466  0.836  H16 2YD 49 
2YD H17 H17 H 0 1 N N N N N N 77.980 -148.517 63.158 -1.214 3.807  -1.661 H17 2YD 50 
2YD H18 H18 H 0 1 N N N N N N 79.727 -148.150 62.958 -1.308 2.045  -1.907 H18 2YD 51 
2YD H19 H19 H 0 1 N N N N N N 79.671 -148.916 60.628 -2.562 2.221  0.482  H19 2YD 52 
2YD H20 H20 H 0 1 N N N N N N 77.892 -149.150 60.710 -2.934 3.845  -0.150 H20 2YD 53 
2YD H21 H21 H 0 1 N N N N N N 79.930 -150.696 62.415 -3.417 2.431  -2.385 H21 2YD 54 
2YD H22 H22 H 0 1 N N N N N N 79.524 -152.606 60.825 -4.937 4.030  -1.380 H22 2YD 55 
2YD H23 H23 H 0 1 N N N N N N 78.528 -151.517 59.801 -5.817 2.545  -1.816 H23 2YD 56 
2YD H24 H24 H 0 1 N N N N N N 80.281 -151.191 60.019 -5.396 2.864  -0.116 H24 2YD 57 
2YD H25 H25 H 0 1 N N N N N N 77.064 -151.637 61.875 -3.631 0.131  -2.039 H25 2YD 58 
2YD H26 H26 H 0 1 N N N N N N 78.195 -151.529 65.931 -4.549 1.923  1.048  H26 2YD 59 
2YD H27 H27 H 0 1 N N N N N N 79.560 -151.816 64.799 -5.696 0.616  1.429  H27 2YD 60 
2YD H28 H28 H 0 1 N N N N N N 78.866 -150.168 64.969 -4.010 0.512  1.990  H28 2YD 61 
2YD H29 H29 H 0 1 N N N N N N 76.105 -151.571 65.334 -5.397 -1.662 0.113  H29 2YD 62 
2YD H30 H30 H 0 1 N N N N N N 76.490 -153.173 64.620 -4.137 -1.722 -1.140 H30 2YD 63 
2YD H31 H31 H 0 1 N N N N N N 75.249 -152.503 62.543 -2.631 -1.275 1.106  H31 2YD 64 
2YD H32 H32 H 0 1 N N N N N N 74.143 -153.833 64.349 -5.001 -3.024 1.908  H32 2YD 65 
2YD H33 H33 H 0 1 N N N N N N 73.608 -152.312 65.140 -3.540 -2.760 2.890  H33 2YD 66 
2YD H34 H34 H 0 1 N N N N N N 72.972 -152.753 63.519 -4.642 -1.404 2.552  H34 2YD 67 
2YD H35 H35 H 0 1 N N N N N N 75.632 -149.994 63.028 -3.347 -4.128 0.793  H35 2YD 68 
2YD H36 H36 H 0 1 N N N N N N 74.238 -150.110 64.155 -3.032 -3.343 -0.751 H36 2YD 69 
2YD H37 H37 H 0 1 N N N N N N 72.858 -150.859 62.192 -1.090 -4.497 0.425  H37 2YD 70 
2YD H38 H38 H 0 1 N N N N N N 74.714 -151.580 60.724 -1.124 -2.044 2.219  H38 2YD 71 
2YD H39 H39 H 0 1 N N N N N N 73.563 -150.471 59.904 -1.599 -3.690 2.699  H39 2YD 72 
2YD H40 H40 H 0 1 N N N N N N 75.159 -149.860 60.459 0.077  -3.358 2.201  H40 2YD 73 
2YD H41 H41 H 0 1 N N N N N N 74.867 -147.577 62.955 -0.678 -0.861 0.884  H41 2YD 74 
2YD H42 H42 H 0 1 N N N N N N 73.451 -146.546 62.558 -0.199 -0.517 -0.790 H42 2YD 75 
2YD H43 H43 H 0 1 N N N N N N 72.704 -148.961 64.157 -0.737 -2.048 -2.349 H43 2YD 76 
2YD H44 H44 H 0 1 N N N N N N 70.951 -148.581 59.135 4.739  -3.901 -1.449 H44 2YD 77 
2YD H45 H45 H 0 1 N N N N N N 70.889 -147.159 58.039 3.486  -4.843 -0.606 H45 2YD 78 
2YD H46 H46 H 0 1 N N N N N N 71.684 -148.676 57.498 3.171  -4.201 -2.236 H46 2YD 79 
# 
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 
2YD O   C   DOUB N N 1  
2YD O1  C1  SING N N 2  
2YD C   C1  SING N N 3  
2YD C   C7  SING N N 4  
2YD C8  C7  SING N N 5  
2YD C1  C2  DOUB N N 6  
2YD C7  C6  DOUB N N 7  
2YD C2  C22 SING N N 8  
2YD C2  C3  SING N N 9  
2YD C6  C3  SING N N 10 
2YD C6  O3  SING N N 11 
2YD C18 C17 SING N N 12 
2YD C10 C9  SING N N 13 
2YD C22 O4  SING N N 14 
2YD C22 C23 SING N N 15 
2YD C3  C4  SING N N 16 
2YD O3  C5  SING N N 17 
2YD C27 C23 SING N N 18 
2YD C19 C17 SING N N 19 
2YD C19 C20 SING N N 20 
2YD O4  C21 SING N N 21 
2YD C23 C24 SING N N 22 
2YD C17 C16 SING N N 23 
2YD C21 C20 SING N N 24 
2YD C21 C25 SING N N 25 
2YD C9  C5  SING N N 26 
2YD C9  C11 SING N N 27 
2YD C5  C4  SING N N 28 
2YD C5  O2  SING N N 29 
2YD C24 C25 SING N N 30 
2YD C24 O5  SING N N 31 
2YD C16 C15 DOUB N E 32 
2YD C25 C26 SING N N 33 
2YD C11 C12 SING N N 34 
2YD C12 C13 SING N N 35 
2YD C12 C14 SING N N 36 
2YD C15 C14 SING N N 37 
2YD C15 C28 SING N N 38 
2YD O1  H1  SING N N 39 
2YD C3  H4  SING N N 40 
2YD C22 H5  SING N N 41 
2YD C23 H6  SING N N 42 
2YD C27 H7  SING N N 43 
2YD C27 H8  SING N N 44 
2YD C27 H9  SING N N 45 
2YD C24 H10 SING N N 46 
2YD O5  H11 SING N N 47 
2YD C25 H12 SING N N 48 
2YD C26 H13 SING N N 49 
2YD C26 H14 SING N N 50 
2YD C26 H15 SING N N 51 
2YD C21 H16 SING N N 52 
2YD C20 H17 SING N N 53 
2YD C20 H18 SING N N 54 
2YD C19 H19 SING N N 55 
2YD C19 H20 SING N N 56 
2YD C17 H21 SING N N 57 
2YD C18 H22 SING N N 58 
2YD C18 H23 SING N N 59 
2YD C18 H24 SING N N 60 
2YD C16 H25 SING N N 61 
2YD C28 H26 SING N N 62 
2YD C28 H27 SING N N 63 
2YD C28 H28 SING N N 64 
2YD C14 H29 SING N N 65 
2YD C14 H30 SING N N 66 
2YD C12 H31 SING N N 67 
2YD C13 H32 SING N N 68 
2YD C13 H33 SING N N 69 
2YD C13 H34 SING N N 70 
2YD C11 H35 SING N N 71 
2YD C11 H36 SING N N 72 
2YD C9  H37 SING N N 73 
2YD C10 H38 SING N N 74 
2YD C10 H39 SING N N 75 
2YD C10 H40 SING N N 76 
2YD C4  H41 SING N N 77 
2YD C4  H42 SING N N 78 
2YD O2  H43 SING N N 79 
2YD C8  H44 SING N N 80 
2YD C8  H45 SING N N 81 
2YD C8  H46 SING N N 82 
# 
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 
2YD SMILES           ACDLabs              12.01 "O=C1C(=C2OC3(O)C(CC(CC(=CC(C)CCC4OC(C(=C1O)C2C3)C(C)C(O)C4C)C)C)C)C"                                                                                                                                                                        
2YD InChI            InChI                1.03  "InChI=1S/C29H44O6/c1-14-8-9-22-18(5)24(30)19(6)28(34-22)23-21-13-29(33,17(4)12-16(3)11-15(2)10-14)35-27(21)20(7)25(31)26(23)32/h10,14,16-19,21-22,24,28,30,32-33H,8-9,11-13H2,1-7H3/b15-10+/t14-,16+,17-,18-,19+,21+,22+,24-,28+,29+/m0/s1" 
2YD InChIKey         InChI                1.03  YTIDBLWNOPLNOU-XOIIUOJKSA-N                                                                                                                                                                                                                  
2YD SMILES_CANONICAL CACTVS               3.385 "C[C@H]1C[C@H](C)[C@@]2(O)C[C@H]3C(=C(C)C(=O)C(=C3[C@@H]4O[C@H](CC[C@H](C)\C=C(/C)C1)[C@H](C)[C@H](O)[C@H]4C)O)O2"                                                                                                                           
2YD SMILES           CACTVS               3.385 "C[CH]1C[CH](C)[C]2(O)C[CH]3C(=C(C)C(=O)C(=C3[CH]4O[CH](CC[CH](C)C=C(C)C1)[CH](C)[CH](O)[CH]4C)O)O2"                                                                                                                                         
2YD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H]\1CC[C@@H]2[C@@H]([C@@H]([C@H]([C@@H](O2)C3=C(C(=O)C(=C4[C@@H]3C[C@@](O4)([C@H](C[C@@H](C/C(=C1)/C)C)C)O)C)O)C)O)C"                                                                                                                   
2YD SMILES           "OpenEye OEToolkits" 1.7.6 "CC1CCC2C(C(C(C(O2)C3=C(C(=O)C(=C4C3CC(O4)(C(CC(CC(=C1)C)C)C)O)C)O)C)O)C"                                                                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           2YD 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           ACDLabs 
_pdbx_chem_comp_identifier.program_version   12.01 
_pdbx_chem_comp_identifier.identifier        "(5R,6R,7S,8R,9R,12S,13E,16S,18S,19R,20aR)-4,7,19-trihydroxy-2,6,8,12,14,16,18-heptamethyl-6,7,8,9,10,11,12,15,16,17,18,19,20,20a-tetradecahydro-1,19:5,9-diepoxybenzo[18]annulen-3(5H)-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
2YD "Create component" 2014-05-01 RCSB 
2YD "Initial release"  2014-07-30 RCSB 
2YD "Modify synonyms"  2021-03-01 PDBE 
2YD "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      2YD 
_pdbx_chem_comp_synonyms.name         Kendomycin 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            2YD 
_pdbx_chem_comp_pcm.modified_residue_id                HIS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C4 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NE2 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
