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 
# 
