data_QOB
# 
_chem_comp.id                                    QOB 
_chem_comp.name                                  "~{N}-[(2~{S},3~{R})-1-[[(5~{S},8~{S},10~{S})-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-5-phenyl-pentanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H40 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Syrbactin inhibitor; HB334" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-07-09 
_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                        504.619 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     QOB 
_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        6ZP6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
QOB C4  C1  C 0 1 Y N N N N N 53.017 -132.007 34.056 9.466  -1.775 -0.441 C4  QOB 1  
QOB C5  C2  C 0 1 Y N N N N N 52.059 -131.343 33.336 10.577 -1.970 -1.240 C5  QOB 2  
QOB C6  C3  C 0 1 Y N N N N N 51.340 -132.006 32.373 11.277 -0.882 -1.727 C6  QOB 3  
QOB C7  C4  C 0 1 Y N N N N N 51.583 -133.344 32.132 10.866 0.400  -1.416 C7  QOB 4  
QOB C8  C5  C 0 1 Y N N N N N 52.545 -134.008 32.867 9.755  0.595  -0.618 C8  QOB 5  
QOB C15 C6  C 0 1 N N N N N N 61.234 -135.189 37.249 -0.726 0.151  0.303  C15 QOB 6  
QOB C17 C7  C 0 1 N N S N N N 61.306 -136.495 39.239 -3.017 -0.679 0.319  C17 QOB 7  
QOB C21 C8  C 0 1 N N N N N N 59.218 -139.250 40.599 -6.150 -2.491 1.059  C21 QOB 8  
QOB C22 C9  C 0 1 N N N N N N 59.687 -139.657 41.952 -7.294 -2.524 0.042  C22 QOB 9  
QOB C24 C10 C 0 1 N N N N N N 61.599 -138.597 43.121 -6.862 -0.324 -0.832 C24 QOB 10 
QOB C26 C11 C 0 1 N N N N N N 62.937 -138.357 43.045 -7.251 1.105  -1.108 C26 QOB 11 
QOB C28 C12 C 0 1 N N S N N N 63.541 -136.185 42.126 -4.978 2.115  -1.345 C28 QOB 12 
QOB C27 C13 C 0 1 N N N N N N 63.327 -136.948 43.390 -6.256 1.725  -2.091 C27 QOB 13 
QOB C29 C14 C 0 1 N N N N N N 63.838 -134.751 42.464 -4.235 3.201  -2.126 C29 QOB 14 
QOB N30 N1  N 0 1 N N N N N N 62.357 -136.258 41.302 -4.120 0.904  -1.229 N30 QOB 15 
QOB C31 C15 C 0 1 N N N N N N 62.444 -136.409 39.961 -3.867 0.541  0.073  C31 QOB 16 
QOB O32 O1  O 0 1 N N N N N N 63.531 -136.469 39.440 -4.316 1.185  0.998  O32 QOB 17 
QOB O25 O2  O 0 1 N N N N N N 60.919 -138.225 44.060 -5.775 -0.744 -1.168 O25 QOB 18 
QOB N23 N2  N 0 1 N N N N N N 61.081 -139.316 42.071 -7.756 -1.137 -0.194 N23 QOB 19 
QOB C19 C16 C 0 1 N N S N N N 59.586 -137.865 40.311 -4.813 -2.415 0.319  C19 QOB 20 
QOB O20 O3  O 0 1 N N N N N N 58.521 -137.329 39.637 -4.340 -3.737 0.053  O20 QOB 21 
QOB C18 C17 C 0 1 N N N N N N 60.750 -137.864 39.388 -3.793 -1.674 1.185  C18 QOB 22 
QOB N16 N3  N 0 1 N N N N N N 61.609 -136.294 37.845 -1.787 -0.285 1.011  N16 QOB 23 
QOB O33 O4  O 0 1 N N N N N N 60.621 -134.311 37.799 -0.759 0.138  -0.909 O33 QOB 24 
QOB C14 C18 C 0 1 N N S N N N 61.540 -135.050 35.798 0.501  0.655  1.019  C14 QOB 25 
QOB C34 C19 C 0 1 N N R N N N 62.610 -134.030 35.675 0.342  2.148  1.315  C34 QOB 26 
QOB C36 C20 C 0 1 N N N N N N 63.856 -134.526 36.338 -0.821 2.353  2.288  C36 QOB 27 
QOB O35 O5  O 0 1 N N N N N N 62.863 -133.890 34.312 1.546  2.649  1.899  O35 QOB 28 
QOB N13 N4  N 0 1 N N N N N N 60.409 -134.438 35.133 1.679  0.449  0.172  N13 QOB 29 
QOB C12 C21 C 0 1 N N N N N N 59.146 -134.727 35.379 2.900  0.336  0.733  C12 QOB 30 
QOB O37 O6  O 0 1 N N N N N N 58.781 -135.549 36.194 3.023  0.406  1.937  O37 QOB 31 
QOB C1  C22 C 0 1 N N N N N N 58.120 -133.963 34.597 4.111  0.123  -0.138 C1  QOB 32 
QOB C2  C23 C 0 1 N N N N N N 56.699 -134.353 34.954 5.360  0.030  0.741  C2  QOB 33 
QOB C41 C24 C 0 1 N N N N N N 55.628 -133.617 34.196 6.591  -0.186 -0.143 C41 QOB 34 
QOB C40 C25 C 0 1 N N N N N N 54.218 -134.008 34.552 7.840  -0.280 0.736  C40 QOB 35 
QOB C3  C26 C 0 1 Y N N N N N 53.256 -133.335 33.833 9.051  -0.492 -0.135 C3  QOB 36 
QOB H1  H1  H 0 1 N N N N N N 53.588 -131.478 34.805 8.919  -2.625 -0.060 H1  QOB 37 
QOB H2  H2  H 0 1 N N N N N N 51.869 -130.297 33.526 10.899 -2.972 -1.482 H2  QOB 38 
QOB H3  H3  H 0 1 N N N N N N 50.586 -131.482 31.805 12.146 -1.035 -2.351 H3  QOB 39 
QOB H4  H4  H 0 1 N N N N N N 51.023 -133.869 31.372 11.414 1.250  -1.796 H4  QOB 40 
QOB H5  H5  H 0 1 N N N N N N 52.739 -135.054 32.684 9.434  1.597  -0.374 H5  QOB 41 
QOB H6  H6  H 0 1 N N N N N N 60.560 -135.759 39.573 -2.765 -1.145 -0.633 H6  QOB 42 
QOB H7  H7  H 0 1 N N N N N N 58.123 -139.348 40.553 -6.260 -1.617 1.701  H7  QOB 43 
QOB H8  H8  H 0 1 N N N N N N 59.677 -139.908 39.846 -6.179 -3.395 1.666  H8  QOB 44 
QOB H9  H9  H 0 1 N N N N N N 59.108 -139.126 42.721 -6.939 -2.955 -0.894 H9  QOB 45 
QOB H10 H10 H 0 1 N N N N N N 59.558 -140.742 42.079 -8.116 -3.122 0.435  H10 QOB 46 
QOB H11 H11 H 0 1 N N N N N N 63.450 -139.038 43.740 -8.252 1.132  -1.539 H11 QOB 47 
QOB H12 H12 H 0 1 N N N N N N 63.268 -138.565 42.017 -7.242 1.671  -0.176 H12 QOB 48 
QOB H13 H13 H 0 1 N N N N N N 64.399 -136.612 41.586 -5.229 2.484  -0.351 H13 QOB 49 
QOB H14 H14 H 0 1 N N N N N N 64.256 -136.955 43.979 -6.016 1.001  -2.870 H14 QOB 50 
QOB H15 H15 H 0 1 N N N N N N 62.525 -136.475 43.976 -6.697 2.613  -2.544 H15 QOB 51 
QOB H16 H16 H 0 1 N N N N N N 64.740 -134.701 43.091 -4.875 4.077  -2.229 H16 QOB 52 
QOB H17 H17 H 0 1 N N N N N N 64.004 -134.183 41.537 -3.326 3.475  -1.592 H17 QOB 53 
QOB H18 H18 H 0 1 N N N N N N 62.987 -134.319 43.011 -3.975 2.823  -3.116 H18 QOB 54 
QOB H19 H19 H 0 1 N N N N N N 61.456 -136.196 41.731 -3.774 0.419  -1.995 H19 QOB 55 
QOB H20 H20 H 0 1 N N N N N N 61.705 -139.619 41.351 -8.632 -0.827 0.084  H20 QOB 56 
QOB H21 H21 H 0 1 N N N N N N 59.821 -137.317 41.235 -4.948 -1.881 -0.621 H21 QOB 57 
QOB H22 H22 H 0 1 N N N N N N 57.760 -137.317 40.205 -4.939 -4.266 -0.493 H22 QOB 58 
QOB H23 H23 H 0 1 N N N N N N 60.429 -138.232 38.402 -3.099 -2.391 1.624  H23 QOB 59 
QOB H24 H24 H 0 1 N N N N N N 61.530 -138.528 39.790 -4.312 -1.137 1.979  H24 QOB 60 
QOB H25 H25 H 0 1 N N N N N N 62.104 -136.996 37.333 -1.736 -0.339 1.978  H25 QOB 61 
QOB H26 H26 H 0 1 N N N N N N 61.830 -136.009 35.345 0.626  0.111  1.954  H26 QOB 62 
QOB H27 H27 H 0 1 N N N N N N 62.289 -133.081 36.130 0.138  2.683  0.387  H27 QOB 63 
QOB H28 H28 H 0 1 N N N N N N 63.676 -134.643 37.417 -0.669 1.734  3.172  H28 QOB 64 
QOB H29 H29 H 0 1 N N N N N N 64.139 -135.497 35.906 -0.868 3.402  2.582  H29 QOB 65 
QOB H30 H30 H 0 1 N N N N N N 64.669 -133.802 36.178 -1.755 2.070  1.803  H30 QOB 66 
QOB H31 H31 H 0 1 N N N N N N 63.546 -133.243 34.181 2.326  2.552  1.336  H31 QOB 67 
QOB H32 H32 H 0 1 N N N N N N 60.599 -133.746 34.437 1.580  0.393  -0.791 H32 QOB 68 
QOB H33 H33 H 0 1 N N N N N N 58.279 -134.156 33.526 3.995  -0.801 -0.703 H33 QOB 69 
QOB H34 H34 H 0 1 N N N N N N 58.251 -132.890 34.799 4.214  0.961  -0.828 H34 QOB 70 
QOB H35 H35 H 0 1 N N N N N N 56.552 -134.160 36.027 5.477  0.954  1.306  H35 QOB 71 
QOB H36 H36 H 0 1 N N N N N N 56.580 -135.428 34.755 5.257  -0.808 1.431  H36 QOB 72 
QOB H37 H37 H 0 1 N N N N N N 55.775 -133.809 33.123 6.474  -1.111 -0.709 H37 QOB 73 
QOB H38 H38 H 0 1 N N N N N N 55.745 -132.542 34.396 6.694  0.651  -0.833 H38 QOB 74 
QOB H39 H39 H 0 1 N N N N N N 54.060 -133.801 35.621 7.956  0.645  1.301  H39 QOB 75 
QOB H40 H40 H 0 1 N N N N N N 54.099 -135.086 34.366 7.736  -1.117 1.426  H40 QOB 76 
# 
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 
QOB C7  C6  DOUB Y N 1  
QOB C7  C8  SING Y N 2  
QOB C6  C5  SING Y N 3  
QOB C8  C3  DOUB Y N 4  
QOB C5  C4  DOUB Y N 5  
QOB C3  C4  SING Y N 6  
QOB C3  C40 SING N N 7  
QOB C41 C40 SING N N 8  
QOB C41 C2  SING N N 9  
QOB O35 C34 SING N N 10 
QOB C1  C2  SING N N 11 
QOB C1  C12 SING N N 12 
QOB N13 C12 SING N N 13 
QOB N13 C14 SING N N 14 
QOB C12 O37 DOUB N N 15 
QOB C34 C14 SING N N 16 
QOB C34 C36 SING N N 17 
QOB C14 C15 SING N N 18 
QOB C15 O33 DOUB N N 19 
QOB C15 N16 SING N N 20 
QOB N16 C17 SING N N 21 
QOB C17 C18 SING N N 22 
QOB C17 C31 SING N N 23 
QOB C18 C19 SING N N 24 
QOB O32 C31 DOUB N N 25 
QOB O20 C19 SING N N 26 
QOB C31 N30 SING N N 27 
QOB C19 C21 SING N N 28 
QOB C21 C22 SING N N 29 
QOB N30 C28 SING N N 30 
QOB C22 N23 SING N N 31 
QOB N23 C24 SING N N 32 
QOB C28 C29 SING N N 33 
QOB C28 C27 SING N N 34 
QOB C26 C24 SING N N 35 
QOB C26 C27 SING N N 36 
QOB C24 O25 DOUB N N 37 
QOB C4  H1  SING N N 38 
QOB C5  H2  SING N N 39 
QOB C6  H3  SING N N 40 
QOB C7  H4  SING N N 41 
QOB C8  H5  SING N N 42 
QOB C17 H6  SING N N 43 
QOB C21 H7  SING N N 44 
QOB C21 H8  SING N N 45 
QOB C22 H9  SING N N 46 
QOB C22 H10 SING N N 47 
QOB C26 H11 SING N N 48 
QOB C26 H12 SING N N 49 
QOB C28 H13 SING N N 50 
QOB C27 H14 SING N N 51 
QOB C27 H15 SING N N 52 
QOB C29 H16 SING N N 53 
QOB C29 H17 SING N N 54 
QOB C29 H18 SING N N 55 
QOB N30 H19 SING N N 56 
QOB N23 H20 SING N N 57 
QOB C19 H21 SING N N 58 
QOB O20 H22 SING N N 59 
QOB C18 H23 SING N N 60 
QOB C18 H24 SING N N 61 
QOB N16 H25 SING N N 62 
QOB C14 H26 SING N N 63 
QOB C34 H27 SING N N 64 
QOB C36 H28 SING N N 65 
QOB C36 H29 SING N N 66 
QOB C36 H30 SING N N 67 
QOB O35 H31 SING N N 68 
QOB N13 H32 SING N N 69 
QOB C1  H33 SING N N 70 
QOB C1  H34 SING N N 71 
QOB C2  H35 SING N N 72 
QOB C2  H36 SING N N 73 
QOB C41 H37 SING N N 74 
QOB C41 H38 SING N N 75 
QOB C40 H39 SING N N 76 
QOB C40 H40 SING N N 77 
# 
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 
QOB InChI            InChI                1.03  "InChI=1S/C26H40N4O6/c1-17-12-13-22(33)27-15-14-20(32)16-21(25(35)28-17)29-26(36)24(18(2)31)30-23(34)11-7-6-10-19-8-4-3-5-9-19/h3-5,8-9,17-18,20-21,24,31-32H,6-7,10-16H2,1-2H3,(H,27,33)(H,28,35)(H,29,36)(H,30,34)/t17-,18+,20-,21-,24-/m0/s1" 
QOB InChIKey         InChI                1.03  WMBRGTCTXHPVLU-KGLBSCIUSA-N                                                                                                                                                                                                                      
QOB SMILES_CANONICAL CACTVS               3.385 "C[C@@H](O)[C@H](NC(=O)CCCCc1ccccc1)C(=O)N[C@H]2C[C@@H](O)CCNC(=O)CC[C@H](C)NC2=O"                                                                                                                                                               
QOB SMILES           CACTVS               3.385 "C[CH](O)[CH](NC(=O)CCCCc1ccccc1)C(=O)N[CH]2C[CH](O)CCNC(=O)CC[CH](C)NC2=O"                                                                                                                                                                      
QOB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1CCC(=O)NCC[C@@H](C[C@@H](C(=O)N1)NC(=O)[C@H]([C@@H](C)O)NC(=O)CCCCc2ccccc2)O"                                                                                                                                                            
QOB SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CCC(=O)NCCC(CC(C(=O)N1)NC(=O)C(C(C)O)NC(=O)CCCCc2ccccc2)O"                                                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           QOB 
_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        "~{N}-[(2~{S},3~{R})-1-[[(5~{S},8~{S},10~{S})-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-5-phenyl-pentanamide" 
# 
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 QOB "Syrbactin inhibitor" ? ? 
2 QOB HB334                 ? ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
QOB "Create component" 2020-07-09 PDBE 
QOB "Modify synonyms"  2020-07-10 PDBE 
QOB "Initial release"  2021-05-19 RCSB 
QOB "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            QOB 
_pdbx_chem_comp_pcm.modified_residue_id                THR 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Lipid/lipid-like 
_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               C27 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG1 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
