data_U3B # _chem_comp.id U3B _chem_comp.name Omadacycline _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H40 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Omadacycline; (4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-24 _chem_comp.pdbx_modified_date 2023-07-28 _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 556.650 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U3B _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 8CA7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 U3B C1 C1 C 0 1 N N N 179.678 120.958 171.743 -7.239 -2.948 0.515 C1 U3B 1 U3B C2 C2 C 0 1 N N N 179.253 119.802 170.823 -8.074 -1.667 0.474 C2 U3B 2 U3B C3 C3 C 0 1 N N N 177.813 119.355 171.129 -9.507 -2.004 0.056 C3 U3B 3 U3B C4 C4 C 0 1 N N N 180.213 118.611 170.958 -8.086 -1.020 1.860 C4 U3B 4 U3B C5 C5 C 0 1 N N N 179.262 120.321 169.371 -7.464 -0.694 -0.538 C5 U3B 5 U3B N1 N1 N 0 1 N N N 180.571 120.689 168.813 -6.089 -0.369 -0.137 N1 U3B 6 U3B C6 C6 C 0 1 N N N 180.557 120.889 167.370 -5.470 0.565 -1.087 C6 U3B 7 U3B C7 C7 C 0 1 Y N N 179.506 121.874 166.939 -4.063 0.874 -0.644 C7 U3B 8 U3B C8 C8 C 0 1 Y N N 179.700 123.226 167.205 -3.796 2.050 0.029 C8 U3B 9 U3B C9 C9 C 0 1 Y N N 178.768 124.185 166.850 -2.502 2.342 0.449 C9 U3B 10 U3B C10 C10 C 0 1 Y N N 177.556 123.790 166.241 -1.472 1.455 0.191 C10 U3B 11 U3B C11 C11 C 0 1 N N N 176.473 124.758 165.874 -0.072 1.752 0.659 C11 U3B 12 U3B C12 C12 C 0 1 N N R 175.085 124.191 166.210 0.942 1.223 -0.353 C12 U3B 13 U3B C13 C13 C 0 1 N N N 173.965 125.217 166.050 2.355 1.371 0.219 C13 U3B 14 U3B C14 C14 C 0 1 N N S 172.574 124.569 165.965 3.347 0.743 -0.760 C14 U3B 15 U3B C15 C15 C 0 1 N N S 171.483 125.672 165.998 4.765 1.169 -0.437 C15 U3B 16 U3B C16 C16 C 0 1 N N N 170.758 125.778 164.664 5.284 0.452 0.777 C16 U3B 17 U3B O1 O1 O 0 1 N N N 169.573 126.182 164.659 6.071 1.001 1.520 O1 U3B 18 U3B C17 C17 C 0 1 N N N 171.433 125.399 163.413 4.838 -0.910 1.058 C17 U3B 19 U3B C18 C18 C 0 1 N N N 172.431 124.448 163.521 3.833 -1.473 0.314 C18 U3B 20 U3B C19 C19 C 0 1 N N R 172.543 123.619 164.767 3.162 -0.755 -0.817 C19 U3B 21 U3B C20 C20 C 0 1 N N N 173.723 122.626 164.783 1.710 -1.130 -0.866 C20 U3B 22 U3B O2 O2 O 0 1 N N N 173.539 121.546 164.221 1.424 -2.289 -1.097 O2 U3B 23 U3B C21 C21 C 0 1 N N N 174.933 122.916 165.400 0.684 -0.230 -0.650 C21 U3B 24 U3B C22 C22 C 0 1 N N N 176.037 122.054 165.355 -0.624 -0.661 -0.772 C22 U3B 25 U3B C23 C23 C 0 1 Y N N 177.318 122.426 165.992 -1.735 0.268 -0.498 C23 U3B 26 U3B C24 C24 C 0 1 Y N N 178.292 121.468 166.353 -3.042 -0.027 -0.908 C24 U3B 27 U3B O3 O3 O 0 1 N N N 178.074 120.156 166.114 -3.308 -1.189 -1.558 O3 U3B 28 U3B O4 O4 O 0 1 N N N 176.001 120.847 164.776 -0.890 -1.926 -1.165 O4 U3B 29 U3B O5 O5 O 0 1 N N N 171.367 122.817 164.811 3.765 -1.203 -2.033 O5 U3B 30 U3B O6 O6 O 0 1 N N N 173.351 124.223 162.593 3.434 -2.719 0.610 O6 U3B 31 U3B C25 C25 C 0 1 N N N 171.066 125.928 162.061 5.468 -1.680 2.143 C25 U3B 32 U3B O7 O7 O 0 1 N N N 170.037 126.570 161.917 5.146 -1.478 3.298 O7 U3B 33 U3B N2 N2 N 0 1 N N N 171.890 125.701 160.853 6.401 -2.609 1.855 N2 U3B 34 U3B N3 N3 N 0 1 N N N 170.560 125.556 167.169 5.632 0.866 -1.583 N3 U3B 35 U3B C26 C26 C 0 1 N N N 171.133 125.951 168.466 5.231 1.639 -2.766 C26 U3B 36 U3B C27 C27 C 0 1 N N N 169.704 124.367 167.285 7.044 1.103 -1.253 C27 U3B 37 U3B N4 N4 N 0 1 N N N 179.061 125.554 167.119 -2.241 3.535 1.133 N4 U3B 38 U3B C28 C28 C 0 1 N N N 179.171 126.512 166.025 -2.505 4.700 0.278 C28 U3B 39 U3B C29 C29 C 0 1 N N N 179.620 126.008 168.387 -3.018 3.609 2.378 C29 U3B 40 U3B H1 H1 H 0 1 N N N 179.680 120.614 172.788 -7.674 -3.641 1.236 H1 U3B 41 U3B H2 H2 H 0 1 N N N 180.688 121.295 171.466 -7.231 -3.409 -0.473 H2 U3B 42 U3B H3 H3 H 0 1 N N N 178.970 121.793 171.633 -6.219 -2.708 0.812 H3 U3B 43 U3B H4 H4 H 0 1 N N N 177.758 118.975 172.160 -10.101 -1.091 0.027 H4 U3B 44 U3B H5 H5 H 0 1 N N N 177.132 120.211 171.017 -9.498 -2.465 -0.932 H5 U3B 45 U3B H6 H6 H 0 1 N N N 177.520 118.559 170.429 -9.941 -2.698 0.777 H6 U3B 46 U3B H7 H7 H 0 1 N N N 180.202 118.246 171.996 -8.520 -1.714 2.581 H7 U3B 47 U3B H8 H8 H 0 1 N N N 179.893 117.804 170.282 -7.065 -0.780 2.158 H8 U3B 48 U3B H9 H9 H 0 1 N N N 181.232 118.930 170.693 -8.680 -0.107 1.831 H9 U3B 49 U3B H10 H10 H 0 1 N N N 178.619 121.213 169.331 -7.456 -1.154 -1.525 H10 U3B 50 U3B H11 H11 H 0 1 N N N 178.836 119.533 168.732 -8.059 0.220 -0.567 H11 U3B 51 U3B H12 H12 H 0 1 N N N 181.221 119.959 169.024 -5.534 -1.206 -0.039 H12 U3B 52 U3B H14 H14 H 0 1 N N N 180.358 119.924 166.881 -5.448 0.113 -2.079 H14 U3B 53 U3B H15 H15 H 0 1 N N N 181.542 121.263 167.055 -6.051 1.487 -1.120 H15 U3B 54 U3B H16 H16 H 0 1 N N N 180.606 123.536 167.704 -4.595 2.747 0.230 H16 U3B 55 U3B H17 H17 H 0 1 N N N 176.525 124.963 164.795 0.052 2.830 0.766 H17 U3B 56 U3B H18 H18 H 0 1 N N N 176.623 125.694 166.433 0.096 1.274 1.624 H18 U3B 57 U3B H19 H19 H 0 1 N N N 175.106 123.900 167.271 0.865 1.799 -1.275 H19 U3B 58 U3B H20 H20 H 0 1 N N N 174.143 125.791 165.129 2.589 2.428 0.348 H20 U3B 59 U3B H21 H21 H 0 1 N N N 173.984 125.897 166.915 2.415 0.863 1.181 H21 U3B 60 U3B H22 H22 H 0 1 N N N 172.443 123.958 166.871 3.110 1.129 -1.751 H22 U3B 61 U3B H23 H23 H 0 1 N N N 172.024 126.621 166.125 4.782 2.243 -0.251 H23 U3B 62 U3B H26 H26 H 0 1 N N N 178.820 119.651 166.414 -3.539 -1.923 -0.973 H26 U3B 63 U3B H27 H27 H 0 1 N N N 175.141 120.701 164.399 -0.898 -2.568 -0.442 H27 U3B 64 U3B H28 H28 H 0 1 N N N 171.590 121.916 164.608 3.681 -2.154 -2.187 H28 U3B 65 U3B H29 H29 H 0 1 N N N 173.930 123.528 162.882 3.839 -3.137 1.383 H29 U3B 66 U3B H30 H30 H 0 1 N N N 171.595 126.067 159.971 6.708 -2.722 0.942 H30 U3B 67 U3B H31 H31 H 0 1 N N N 172.742 125.181 160.919 6.766 -3.164 2.562 H31 U3B 68 U3B H33 H33 H 0 1 N N N 170.376 125.828 169.255 5.189 2.698 -2.511 H33 U3B 69 U3B H34 H34 H 0 1 N N N 172.003 125.316 168.691 5.958 1.486 -3.564 H34 U3B 70 U3B H35 H35 H 0 1 N N N 171.449 127.004 168.422 4.248 1.306 -3.101 H35 U3B 71 U3B H36 H36 H 0 1 N N N 169.093 124.442 168.197 7.334 0.466 -0.418 H36 U3B 72 U3B H37 H37 H 0 1 N N N 169.045 124.302 166.406 7.663 0.870 -2.119 H37 U3B 73 U3B H38 H38 H 0 1 N N N 170.333 123.466 167.339 7.182 2.149 -0.978 H38 U3B 74 U3B H39 H39 H 0 1 N N N 179.400 127.508 166.431 -3.565 4.734 0.027 H39 U3B 75 U3B H40 H40 H 0 1 N N N 179.977 126.200 165.344 -2.228 5.611 0.809 H40 U3B 76 U3B H41 H41 H 0 1 N N N 178.220 126.550 165.474 -1.918 4.621 -0.636 H41 U3B 77 U3B H42 H42 H 0 1 N N N 179.491 125.223 169.147 -2.804 2.734 2.992 H42 U3B 78 U3B H43 H43 H 0 1 N N N 180.691 126.222 168.259 -2.745 4.512 2.924 H43 U3B 79 U3B H44 H44 H 0 1 N N N 179.099 126.921 168.711 -4.082 3.635 2.141 H44 U3B 80 # 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 U3B N2 C25 SING N N 1 U3B O7 C25 DOUB N N 2 U3B C25 C17 SING N N 3 U3B O6 C18 SING N N 4 U3B C17 C18 DOUB N N 5 U3B C17 C16 SING N N 6 U3B C18 C19 SING N N 7 U3B O2 C20 DOUB N N 8 U3B O1 C16 DOUB N N 9 U3B C16 C15 SING N N 10 U3B C19 C20 SING N N 11 U3B C19 O5 SING N N 12 U3B C19 C14 SING N N 13 U3B O4 C22 SING N N 14 U3B C20 C21 SING N N 15 U3B C22 C21 DOUB N N 16 U3B C22 C23 SING N N 17 U3B C21 C12 SING N N 18 U3B C11 C12 SING N N 19 U3B C11 C10 SING N N 20 U3B C14 C15 SING N N 21 U3B C14 C13 SING N N 22 U3B C23 C10 DOUB Y N 23 U3B C23 C24 SING Y N 24 U3B C15 N3 SING N N 25 U3B C28 N4 SING N N 26 U3B C13 C12 SING N N 27 U3B O3 C24 SING N N 28 U3B C10 C9 SING Y N 29 U3B C24 C7 DOUB Y N 30 U3B C9 N4 SING N N 31 U3B C9 C8 DOUB Y N 32 U3B C7 C8 SING Y N 33 U3B C7 C6 SING N N 34 U3B N4 C29 SING N N 35 U3B N3 C27 SING N N 36 U3B N3 C26 SING N N 37 U3B C6 N1 SING N N 38 U3B N1 C5 SING N N 39 U3B C5 C2 SING N N 40 U3B C2 C4 SING N N 41 U3B C2 C3 SING N N 42 U3B C2 C1 SING N N 43 U3B C1 H1 SING N N 44 U3B C1 H2 SING N N 45 U3B C1 H3 SING N N 46 U3B C3 H4 SING N N 47 U3B C3 H5 SING N N 48 U3B C3 H6 SING N N 49 U3B C4 H7 SING N N 50 U3B C4 H8 SING N N 51 U3B C4 H9 SING N N 52 U3B C5 H10 SING N N 53 U3B C5 H11 SING N N 54 U3B N1 H12 SING N N 55 U3B C6 H14 SING N N 56 U3B C6 H15 SING N N 57 U3B C8 H16 SING N N 58 U3B C11 H17 SING N N 59 U3B C11 H18 SING N N 60 U3B C12 H19 SING N N 61 U3B C13 H20 SING N N 62 U3B C13 H21 SING N N 63 U3B C14 H22 SING N N 64 U3B C15 H23 SING N N 65 U3B O3 H26 SING N N 66 U3B O4 H27 SING N N 67 U3B O5 H28 SING N N 68 U3B O6 H29 SING N N 69 U3B N2 H30 SING N N 70 U3B N2 H31 SING N N 71 U3B C26 H33 SING N N 72 U3B C26 H34 SING N N 73 U3B C26 H35 SING N N 74 U3B C27 H36 SING N N 75 U3B C27 H37 SING N N 76 U3B C27 H38 SING N N 77 U3B C28 H39 SING N N 78 U3B C28 H40 SING N N 79 U3B C28 H41 SING N N 80 U3B C29 H42 SING N N 81 U3B C29 H43 SING N N 82 U3B C29 H44 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 U3B InChI InChI 1.06 "InChI=1S/C29H40N4O7/c1-28(2,3)12-31-11-14-10-17(32(4)5)15-8-13-9-16-21(33(6)7)24(36)20(27(30)39)26(38)29(16,40)25(37)18(13)23(35)19(15)22(14)34/h10,13,16,21,31,34-35,38,40H,8-9,11-12H2,1-7H3,(H2,30,39)/t13-,16-,21-,29-/m0/s1" U3B InChIKey InChI 1.06 VJYKVCURWJGLPG-IQZGDKDPSA-N U3B SMILES_CANONICAL CACTVS 3.385 "CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4c(cc(CNCC(C)(C)C)c(O)c4C(=C3C(=O)[C@]2(O)C(=C(C(N)=O)C1=O)O)O)N(C)C" U3B SMILES CACTVS 3.385 "CN(C)[CH]1[CH]2C[CH]3Cc4c(cc(CNCC(C)(C)C)c(O)c4C(=C3C(=O)[C]2(O)C(=C(C(N)=O)C1=O)O)O)N(C)C" U3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)CNCc1cc(c2c(c1O)C(=C3[C@@H](C2)C[C@H]4[C@@H](C(=O)C(=C([C@]4(C3=O)O)O)C(=O)N)N(C)C)O)N(C)C" U3B SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C)CNCc1cc(c2c(c1O)C(=C3C(C2)CC4C(C(=O)C(=C(C4(C3=O)O)O)C(=O)N)N(C)C)O)N(C)C" # _pdbx_chem_comp_identifier.comp_id U3B _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(4~{S},4~{a}~{S},5~{a}~{R},12~{a}~{R})-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12~{a}-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4~{a},5,5~{a},6-tetrahydro-4~{H}-tetracene-2-carboxamide" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 U3B Omadacycline DRUGBANK ? 2 U3B "(4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide" PDB ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site U3B "Create component" 2023-01-24 PDBE U3B "Modify name" 2023-01-26 PDBE U3B "Modify aromatic_flag" 2023-07-25 PDBE U3B "Initial release" 2023-08-02 RCSB #