data_GDT # _chem_comp.id GDT _chem_comp.name ;(2E,4E)-N-[(2S,3R)-3-hydroxy-1-[[(3Z,5S,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]amino]-1-ox obutan-2-yl]dodeca-2,4-dienamide ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H44 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Glidobactin A" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-11-20 _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 520.661 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDT _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 3BDM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 GDT C1 C1 C 0 1 N N N N N N 10.901 -164.383 32.505 -3.020 0.178 -0.593 C1 GDT 1 GDT C2 C2 C 0 1 N N N N N N 12.218 -164.040 32.576 -4.080 0.727 0.041 C2 GDT 2 GDT C3 C3 C 0 1 N N N N N N 13.186 -164.725 31.688 -5.400 0.708 -0.591 C3 GDT 3 GDT C4 C4 C 0 1 N N N N N N 14.532 -164.504 31.620 -6.447 1.249 0.034 C4 GDT 4 GDT C5 C5 C 0 1 N N N N N N 15.327 -165.285 30.603 -7.806 1.230 -0.616 C5 GDT 5 GDT C6 C6 C 0 1 N N N N N N 16.715 -164.765 30.281 -8.816 0.578 0.331 C6 GDT 6 GDT O37 O37 O 0 1 N N N N N N 10.171 -162.838 34.100 -1.558 0.707 1.134 O37 GDT 7 GDT C12 C12 C 0 1 N N N N N N 9.837 -163.755 33.313 -1.701 0.197 0.038 C12 GDT 8 GDT N13 N13 N 0 1 N N N N N N 8.516 -164.119 33.174 -0.643 -0.350 -0.594 N13 GDT 9 GDT C14 C14 C 0 1 N N S N N N 7.435 -163.397 33.961 0.678 -0.331 0.039 C14 GDT 10 GDT C34 C34 C 0 1 N N R N N N 5.949 -163.782 33.547 0.809 -1.528 0.982 C34 GDT 11 GDT C36 C36 C 0 1 N N N N N N 5.729 -163.700 32.018 -0.285 -1.458 2.049 C36 GDT 12 GDT O35 O35 O 0 1 N N N N N N 5.639 -165.106 34.045 0.671 -2.739 0.237 O35 GDT 13 GDT C15 C15 C 0 1 N N N N N N 7.666 -163.515 35.485 1.744 -0.409 -1.023 C15 GDT 14 GDT O33 O33 O 0 1 N N N N N N 8.091 -164.547 35.953 1.446 -0.699 -2.162 O33 GDT 15 GDT N16 N16 N 0 1 N N N N N N 7.418 -162.459 36.206 3.030 -0.157 -0.707 N16 GDT 16 GDT C17 C17 C 0 1 N N S N N N 7.641 -162.449 37.622 4.080 -0.337 -1.713 C17 GDT 17 GDT C31 C31 C 0 1 N N N N N N 6.401 -162.820 38.423 5.193 -1.170 -1.136 C31 GDT 18 GDT O32 O32 O 0 1 N N N N N N 5.281 -162.424 38.011 6.239 -1.284 -1.739 O32 GDT 19 GDT N30 N30 N 0 1 N N N N N N 6.575 -163.464 39.644 5.028 -1.794 0.057 N30 GDT 20 GDT C28 C28 C 0 1 N N S N N N 5.442 -163.695 40.544 6.250 -2.292 0.726 C28 GDT 21 GDT C29 C29 C 0 1 N N N N N N 5.151 -165.214 40.666 7.258 -2.769 -0.322 C29 GDT 22 GDT C27 C27 C 0 1 N N N N N N 5.809 -163.086 41.891 6.836 -1.143 1.518 C27 GDT 23 GDT C26 C26 C 0 1 N N N N N N 6.154 -161.540 41.786 6.850 0.067 0.974 C26 GDT 24 GDT C24 C24 C 0 1 N N N N N N 7.486 -161.215 42.433 7.380 1.232 1.697 C24 GDT 25 GDT O25 O25 O 0 1 N N N N N N 7.819 -161.963 43.375 7.970 1.095 2.751 O25 GDT 26 GDT N23 N23 N 0 1 N N N N N N 8.322 -160.200 42.075 7.195 2.467 1.158 N23 GDT 27 GDT C22 C22 C 0 1 N N N N N N 8.120 -159.240 41.026 6.413 2.563 -0.090 C22 GDT 28 GDT C21 C21 C 0 1 N N N N N N 9.075 -159.531 39.858 5.005 2.020 0.158 C21 GDT 29 GDT C19 C19 C 0 1 N N S N N N 9.009 -160.956 39.318 4.181 2.097 -1.126 C19 GDT 30 GDT O20 O20 O 0 1 N N N N N N 10.332 -161.299 38.938 2.802 1.890 -0.816 O20 GDT 31 GDT C18 C18 C 0 1 N N N N N N 8.097 -161.018 38.083 4.644 1.029 -2.116 C18 GDT 32 GDT C7 C7 C 0 1 N N N N N N 17.819 -165.766 30.749 -10.196 0.558 -0.329 C7 GDT 33 GDT C8 C8 C 0 1 N N N N N N 19.288 -165.342 30.468 -11.205 -0.094 0.618 C8 GDT 34 GDT C9 C9 C 0 1 N N N N N N 20.189 -166.495 31.037 -12.585 -0.113 -0.043 C9 GDT 35 GDT C10 C10 C 0 1 N N N N N N 21.735 -166.211 30.781 -13.594 -0.765 0.905 C10 GDT 36 GDT C11 C11 C 0 1 N N N N N N 22.552 -167.450 31.387 -14.974 -0.785 0.244 C11 GDT 37 GDT H1 H1 H 0 1 N N N N N N 10.618 -165.163 31.814 -3.148 -0.278 -1.564 H1 GDT 38 GDT H2 H2 H 0 1 N N N N N N 12.551 -163.281 33.269 -3.954 1.179 1.013 H2 GDT 39 GDT H3 H3 H 0 1 N N N N N N 12.785 -165.478 31.025 -5.527 0.256 -1.564 H3 GDT 40 GDT H4 H4 H 0 1 N N N N N N 15.013 -163.792 32.274 -6.320 1.701 1.007 H4 GDT 41 GDT H5 H5 H 0 1 N N N N N N 15.446 -166.305 30.998 -8.119 2.251 -0.834 H5 GDT 42 GDT H5A H5A H 0 1 N N N N N N 14.759 -165.209 29.664 -7.757 0.659 -1.543 H5A GDT 43 GDT H6 H6 H 0 1 N N N N N N 16.799 -164.626 29.193 -8.502 -0.443 0.549 H6 GDT 44 GDT H6A H6A H 0 1 N N N N N N 16.861 -163.812 30.811 -8.865 1.149 1.258 H6A GDT 45 GDT HN13 HN13 H 0 0 N N N N N N 8.267 -164.862 32.552 -0.757 -0.756 -1.467 HN13 GDT 46 GDT H14 H14 H 0 1 N N N N N N 7.534 -162.337 33.684 0.797 0.593 0.605 H14 GDT 47 GDT H34 H34 H 0 1 N N N N N N 5.265 -163.050 34.001 1.787 -1.507 1.462 H34 GDT 48 GDT H36 H36 H 0 1 N N N N N N 4.650 -163.681 31.803 -1.259 -1.604 1.582 H36 GDT 49 GDT H36A H36A H 0 0 N N N N N N 6.197 -162.784 31.629 -0.118 -2.239 2.792 H36A GDT 50 GDT H36B H36B H 0 0 N N N N N N 6.183 -164.578 31.535 -0.257 -0.483 2.535 H36B GDT 51 GDT HO35 HO35 H 0 0 N N N N N N 5.571 -165.711 33.316 1.333 -2.851 -0.459 HO35 GDT 52 GDT HN16 HN16 H 0 0 N N N N N N 7.064 -161.636 35.761 3.260 0.144 0.186 HN16 GDT 53 GDT H17 H17 H 0 1 N N N N N N 8.418 -163.203 37.814 3.666 -0.836 -2.589 H17 GDT 54 GDT HN30 HN30 H 0 0 N N N N N N 7.487 -163.774 39.911 4.150 -1.909 0.454 HN30 GDT 55 GDT H28 H28 H 0 1 N N N N N N 4.525 -163.227 40.157 5.997 -3.114 1.396 H28 GDT 56 GDT H29 H29 H 0 1 N N N N N N 5.082 -165.657 39.661 7.763 -1.907 -0.758 H29 GDT 57 GDT H29A H29A H 0 0 N N N N N N 5.965 -165.699 41.225 7.993 -3.420 0.151 H29A GDT 58 GDT H29B H29B H 0 0 N N N N N N 4.200 -165.363 41.198 6.736 -3.319 -1.105 H29B GDT 59 GDT H27 H27 H 0 1 N N N N N N 5.832 -163.644 42.815 7.224 -1.316 2.505 H27 GDT 60 GDT H26 H26 H 0 1 N N N N N N 5.517 -160.808 41.311 6.481 0.198 -0.037 H26 GDT 61 GDT HN23 HN23 H 0 0 N N N N N N 9.169 -160.114 42.600 7.564 3.258 1.580 HN23 GDT 62 GDT H22 H22 H 0 1 N N N N N N 7.081 -159.303 40.671 6.352 3.605 -0.402 H22 GDT 63 GDT H22A H22A H 0 0 N N N N N N 8.321 -158.231 41.415 6.898 1.976 -0.869 H22A GDT 64 GDT H21 H21 H 0 1 N N N N N N 8.816 -158.848 39.035 5.070 0.982 0.484 H21 GDT 65 GDT H21A H21A H 0 0 N N N N N N 10.095 -159.390 40.245 4.521 2.612 0.934 H21A GDT 66 GDT H19 H19 H 0 1 N N N N N N 8.605 -161.644 40.075 4.306 3.082 -1.576 H19 GDT 67 GDT HO20 HO20 H 0 0 N N N N N N 10.381 -161.376 37.992 2.435 2.540 -0.201 HO20 GDT 68 GDT H18 H18 H 0 1 N N N N N N 8.651 -160.567 37.246 5.733 0.984 -2.118 H18 GDT 69 GDT H18A H18A H 0 0 N N N N N N 7.175 -160.491 38.369 4.292 1.285 -3.115 H18A GDT 70 GDT H7 H7 H 0 1 N N N N N N 17.714 -165.884 31.838 -10.509 1.579 -0.547 H7 GDT 71 GDT H7A H7A H 0 1 N N N N N N 17.656 -166.686 30.168 -10.146 -0.012 -1.257 H7A GDT 72 GDT H8 H8 H 0 1 N N N N N N 19.455 -165.217 29.388 -10.892 -1.115 0.836 H8 GDT 73 GDT H8A H8A H 0 1 N N N N N N 19.524 -164.378 30.942 -11.254 0.477 1.545 H8A GDT 74 GDT H9 H9 H 0 1 N N N N N N 20.019 -166.575 32.121 -12.898 0.908 -0.261 H9 GDT 75 GDT H9A H9A H 0 1 N N N N N N 19.920 -167.429 30.523 -12.536 -0.684 -0.970 H9A GDT 76 GDT H10 H10 H 0 1 N N N N N N 21.931 -166.117 29.703 -13.281 -1.786 1.122 H10 GDT 77 GDT H10A H10A H 0 0 N N N N N N 22.042 -165.270 31.261 -13.644 -0.194 1.832 H10A GDT 78 GDT H11 H11 H 0 1 N N N N N N 22.739 -168.189 30.594 -14.925 -1.355 -0.683 H11 GDT 79 GDT H11A H11A H 0 0 N N N N N N 23.512 -167.094 31.790 -15.693 -1.249 0.919 H11A GDT 80 GDT H11B H11B H 0 0 N N N N N N 21.966 -167.917 32.192 -15.288 0.236 0.026 H11B GDT 81 # 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 GDT C1 C2 DOUB N E 1 GDT C1 C12 SING N N 2 GDT C2 C3 SING N N 3 GDT C3 C4 DOUB N N 4 GDT C4 C5 SING N N 5 GDT C5 C6 SING N E 6 GDT C6 C7 SING N N 7 GDT O37 C12 DOUB N N 8 GDT C12 N13 SING N N 9 GDT N13 C14 SING N N 10 GDT C14 C34 SING N N 11 GDT C14 C15 SING N N 12 GDT C34 C36 SING N N 13 GDT C34 O35 SING N N 14 GDT C15 O33 DOUB N N 15 GDT C15 N16 SING N N 16 GDT N16 C17 SING N N 17 GDT C17 C31 SING N N 18 GDT C17 C18 SING N N 19 GDT C31 O32 DOUB N N 20 GDT C31 N30 SING N N 21 GDT N30 C28 SING N N 22 GDT C28 C29 SING N N 23 GDT C28 C27 SING N N 24 GDT C27 C26 DOUB N N 25 GDT C26 C24 SING N N 26 GDT C24 O25 DOUB N N 27 GDT C24 N23 SING N N 28 GDT N23 C22 SING N N 29 GDT C22 C21 SING N N 30 GDT C21 C19 SING N N 31 GDT C19 O20 SING N N 32 GDT C19 C18 SING N N 33 GDT C7 C8 SING N N 34 GDT C8 C9 SING N N 35 GDT C9 C10 SING N N 36 GDT C10 C11 SING N N 37 GDT C1 H1 SING N N 38 GDT C2 H2 SING N N 39 GDT C3 H3 SING N N 40 GDT C4 H4 SING N N 41 GDT C5 H5 SING N N 42 GDT C5 H5A SING N N 43 GDT C6 H6 SING N N 44 GDT C6 H6A SING N N 45 GDT N13 HN13 SING N N 46 GDT C14 H14 SING N E 47 GDT C34 H34 SING N N 48 GDT C36 H36 SING N N 49 GDT C36 H36A SING N N 50 GDT C36 H36B SING N N 51 GDT O35 HO35 SING N N 52 GDT N16 HN16 SING N N 53 GDT C17 H17 SING N N 54 GDT N30 HN30 SING N N 55 GDT C28 H28 SING N N 56 GDT C29 H29 SING N N 57 GDT C29 H29A SING N N 58 GDT C29 H29B SING N N 59 GDT C27 H27 SING N N 60 GDT C26 H26 SING N N 61 GDT N23 HN23 SING N N 62 GDT C22 H22 SING N N 63 GDT C22 H22A SING N N 64 GDT C21 H21 SING N N 65 GDT C21 H21A SING N N 66 GDT C19 H19 SING N N 67 GDT O20 HO20 SING N N 68 GDT C18 H18 SING N N 69 GDT C18 H18A SING N N 70 GDT C7 H7 SING N N 71 GDT C7 H7A SING N N 72 GDT C8 H8 SING N N 73 GDT C8 H8A SING N N 74 GDT C9 H9 SING N N 75 GDT C9 H9A SING N N 76 GDT C10 H10 SING N N 77 GDT C10 H10A SING N N 78 GDT C11 H11 SING N N 79 GDT C11 H11A SING N N 80 GDT C11 H11B SING N N 81 # 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 GDT SMILES ACDLabs 10.04 "O=C(\C=C\C=C\CCCCCCC)NC(C(=O)NC1C(=O)NC(C=CC(=O)NCCC(O)C1)C)C(O)C" GDT SMILES_CANONICAL CACTVS 3.341 "CCCCCCC/C=C/C=C/C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@H]1C[C@@H](O)CCNC(=O)/C=C/[C@H](C)NC1=O" GDT SMILES CACTVS 3.341 "CCCCCCCC=CC=CC(=O)N[CH]([CH](C)O)C(=O)N[CH]1C[CH](O)CCNC(=O)C=C[CH](C)NC1=O" GDT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCCCCCC\C=C\C=C\C(=O)N[C@@H]([C@@H](C)O)C(=O)N[C@H]1C[C@H](CCNC(=O)C=C[C@@H](NC1=O)C)O" GDT SMILES "OpenEye OEToolkits" 1.5.0 "CCCCCCCC=CC=CC(=O)NC(C(C)O)C(=O)NC1CC(CCNC(=O)C=CC(NC1=O)C)O" GDT InChI InChI 1.03 "InChI=1S/C27H44N4O6/c1-4-5-6-7-8-9-10-11-12-13-24(35)31-25(20(3)32)27(37)30-22-18-21(33)16-17-28-23(34)15-14-19(2)29-26(22)36/h10-15,19-22,25,32-33H,4-9,16-18H2,1-3H3,(H,28,34)(H,29,36)(H,30,37)(H,31,35)/b11-10+,13-12+,15-14+/t19-,20+,21-,22-,25-/m0/s1" GDT InChIKey InChI 1.03 TYGJUQYJMIOZLZ-HXSKNMNHSA-N # 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 GDT "SYSTEMATIC NAME" ACDLabs 10.04 "(2E,4E)-N-[(1S,2R)-2-hydroxy-1-{[(3E,5S,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]carbamoyl}propyl]dodeca-2,4-dienamide" GDT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2E,4E)-N-[(2S,3R)-3-hydroxy-1-[[(5S,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]amino]-1-oxo-butan-2-yl]dodeca-2,4-dienamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GDT "Create component" 2007-11-20 PDBJ GDT "Modify descriptor" 2011-06-04 RCSB GDT "Modify synonyms" 2020-06-05 PDBE GDT "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GDT _pdbx_chem_comp_synonyms.name "Glidobactin A" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id GDT _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 ? #