data_VBN # _chem_comp.id VBN _chem_comp.name ;(4S,5R)-N-{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-N-[3-({[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-met hyl-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C35 H39 N5 O11" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms vibriobactin _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-04-06 _chem_comp.pdbx_modified_date 2020-06-17 _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 705.711 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VBN _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 3R5T _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 VBN C C C 0 1 N N N 24.588 18.115 4.483 -1.903 -1.508 -1.108 C VBN 1 VBN N N N 0 1 N N N 23.568 16.049 5.538 -2.233 -3.577 0.176 N VBN 2 VBN O O O 0 1 N N N 23.748 18.830 4.918 -2.810 -1.702 -1.890 O VBN 3 VBN CA CA C 0 1 N N S 24.435 16.600 4.511 -1.234 -2.673 -0.427 CA VBN 4 VBN CB CB C 0 1 N N R 23.788 15.996 3.208 -0.546 -3.598 -1.461 CB VBN 5 VBN CAB CAB C 0 1 N N N 31.692 13.467 5.941 6.025 -0.909 -2.725 CAB VBN 6 VBN OAC OAC O 0 1 N N N 26.684 21.539 8.282 -5.739 4.574 -1.619 OAC VBN 7 VBN OAD OAD O 0 1 N N N 28.433 14.866 3.041 4.597 0.831 1.061 OAD VBN 8 VBN OAF OAF O 0 1 N N N 24.538 16.083 9.645 -9.819 6.771 0.373 OAF VBN 9 VBN OAG OAG O 0 1 N N N 19.889 15.596 9.238 -5.722 -6.728 2.235 OAG VBN 10 VBN OAH OAH O 0 1 N N N 23.735 13.727 7.898 10.585 3.831 2.474 OAH VBN 11 VBN OAI OAI O 0 1 N N N 25.047 17.727 7.615 -7.668 6.116 -1.217 OAI VBN 12 VBN OAJ OAJ O 0 1 N N N 22.152 16.078 7.807 -4.250 -4.539 1.447 OAJ VBN 13 VBN OAK OAK O 0 1 N N N 25.947 14.843 6.787 8.186 3.151 1.307 OAK VBN 14 VBN CAL CAL C 0 1 Y N N 25.790 19.058 11.535 -8.535 3.852 2.135 CAL VBN 15 VBN CAM CAM C 0 1 Y N N 18.780 14.917 5.746 -3.086 -8.342 0.306 CAM VBN 16 VBN CAN CAN C 0 1 Y N N 25.960 10.769 7.560 11.564 0.875 0.584 CAN VBN 17 VBN CAO CAO C 0 1 Y N N 25.265 17.746 11.282 -9.325 4.942 1.809 CAO VBN 18 VBN CAP CAP C 0 1 Y N N 18.745 15.043 7.164 -4.217 -8.166 1.085 CAP VBN 19 VBN CAQ CAQ C 0 1 Y N N 24.813 11.552 7.916 11.636 1.982 1.413 CAQ VBN 20 VBN CAR CAR C 0 1 Y N N 26.066 19.960 10.443 -7.457 3.513 1.347 CAR VBN 21 VBN CAS CAS C 0 1 Y N N 19.953 15.199 5.031 -2.341 -7.253 -0.095 CAS VBN 22 VBN CAT CAT C 0 1 Y N N 27.074 11.368 6.918 10.369 0.524 -0.006 CAT VBN 23 VBN CAU CAU C 0 1 N N N 26.385 21.003 4.469 -3.394 1.260 -0.571 CAU VBN 24 VBN CAV CAV C 0 1 N N N 27.998 18.493 2.654 0.923 0.142 -0.833 CAV VBN 25 VBN CAW CAW C 0 1 N N N 25.550 21.343 5.715 -4.088 2.493 -1.152 CAW VBN 26 VBN CAX CAX C 0 1 N N N 29.161 17.545 2.279 2.128 0.382 0.078 CAX VBN 27 VBN CAY CAY C 0 1 N N N 25.699 20.103 3.439 -2.197 0.887 -1.448 CAY VBN 28 VBN CAZ CAZ C 0 1 N N N 26.717 17.787 3.130 -0.337 -0.021 0.020 CAZ VBN 29 VBN NBB NBB N 0 1 N N N 25.474 20.319 6.754 -5.234 2.850 -0.312 NBB VBN 30 VBN NBC NBC N 0 1 N N N 29.649 16.829 3.456 3.334 0.539 -0.739 NBC VBN 31 VBN NBD NBD N 0 1 N N N 28.453 14.752 6.041 6.841 1.578 -0.219 NBD VBN 32 VBN OBF OBF O 0 1 N N N 29.332 12.608 5.689 7.803 -0.153 -1.217 OBF VBN 33 VBN CBG CBG C 0 1 N N N 26.079 20.553 8.045 -6.000 3.912 -0.633 CBG VBN 34 VBN CBH CBH C 0 1 N N N 29.181 15.472 3.753 4.525 0.761 -0.147 CBH VBN 35 VBN CBJ CBJ C 0 1 N N N 22.254 16.061 4.950 -1.929 -4.797 -0.144 CBJ VBN 36 VBN CBK CBK C 0 1 Y N N 25.020 17.340 9.938 -9.038 5.702 0.688 CBK VBN 37 VBN CBL CBL C 0 1 Y N N 19.893 15.461 7.862 -4.610 -6.894 1.470 CBL VBN 38 VBN CBM CBM C 0 1 Y N N 24.820 12.913 7.620 10.507 2.746 1.658 CBM VBN 39 VBN CBN CBN C 0 1 Y N N 25.273 18.191 8.902 -7.952 5.373 -0.117 CBN VBN 40 VBN CBO CBO C 0 1 Y N N 21.002 15.727 7.169 -3.867 -5.787 1.072 CBO VBN 41 VBN CBP CBP C 0 1 Y N N 25.898 13.485 7.000 9.295 2.403 1.069 CBP VBN 42 VBN CBQ CBQ C 0 1 Y N N 25.822 19.557 9.170 -7.154 4.271 0.213 CBQ VBN 43 VBN CBR CBR C 0 1 Y N N 21.045 15.570 5.707 -2.725 -5.966 0.285 CBR VBN 44 VBN CBS CBS C 0 1 Y N N 27.079 12.687 6.656 9.223 1.285 0.232 CBS VBN 45 VBN CBU CBU C 0 1 N N R 30.381 13.539 5.178 6.396 -0.455 -1.312 CBU VBN 46 VBN CBW CBW C 0 1 N N N 28.173 13.360 5.877 7.940 0.912 -0.399 CBW VBN 47 VBN CBX CBX C 0 1 N N S 29.584 14.936 5.121 5.766 0.921 -0.987 CBX VBN 48 VBN NBY NBY N 0 1 N N N 25.708 18.666 3.729 -1.491 -0.250 -0.853 NBY VBN 49 VBN OG1 OG1 O 0 1 N N N 22.339 15.881 3.553 -0.818 -4.900 -0.904 OG1 VBN 50 VBN CG2 CG2 C 0 1 N N N 24.469 14.808 2.547 0.959 -3.330 -1.521 CG2 VBN 51 VBN HA HA H 0 1 N N N 25.489 16.330 4.672 -0.521 -2.327 0.321 HA VBN 52 VBN HB HB H 0 1 N N N 23.943 16.656 2.342 -1.001 -3.490 -2.445 HB VBN 53 VBN HAB HAB H 0 1 N N N 32.409 14.179 5.506 6.573 -1.820 -2.969 HAB VBN 54 VBN HABA HABA H 0 0 N N N 31.516 13.722 6.996 4.954 -1.106 -2.775 HABA VBN 55 VBN HABB HABB H 0 0 N N N 32.100 12.448 5.873 6.285 -0.127 -3.438 HABB VBN 56 VBN HOAF HOAF H 0 0 N N N 24.438 15.993 8.705 -9.525 7.603 0.770 HOAF VBN 57 VBN HOAG HOAG H 0 0 N N N 20.745 15.885 9.531 -5.551 -6.749 3.187 HOAG VBN 58 VBN HOAH HOAH H 0 0 N N N 23.928 14.617 7.626 10.801 4.654 2.015 HOAH VBN 59 VBN HOAI HOAI H 0 0 N N N 25.260 18.410 6.990 -7.066 6.854 -1.048 HOAI VBN 60 VBN HOAJ HOAJ H 0 0 N N N 22.836 16.230 7.166 -3.868 -4.246 2.286 HOAJ VBN 61 VBN HOAK HOAK H 0 0 N N N 26.760 15.066 6.348 8.059 3.875 0.679 HOAK VBN 62 VBN HAL HAL H 0 1 N N N 25.980 19.372 12.551 -8.764 3.266 3.013 HAL VBN 63 VBN HAM HAM H 0 1 N N N 17.894 14.601 5.216 -2.784 -9.337 0.014 HAM VBN 64 VBN HAN HAN H 0 1 N N N 25.976 9.712 7.783 12.450 0.287 0.395 HAN VBN 65 VBN HAO HAO H 0 1 N N N 25.058 17.074 12.101 -10.168 5.200 2.432 HAO VBN 66 VBN HAP HAP H 0 1 N N N 17.837 14.818 7.704 -4.795 -9.024 1.395 HAP VBN 67 VBN HAQ HAQ H 0 1 N N N 23.963 11.097 8.403 12.577 2.250 1.871 HAQ VBN 68 VBN HAR HAR H 0 1 N N N 26.463 20.946 10.637 -6.845 2.662 1.607 HAR VBN 69 VBN HAS HAS H 0 1 N N N 19.974 15.118 3.954 -1.460 -7.397 -0.703 HAS VBN 70 VBN HAT HAT H 0 1 N N N 27.923 10.762 6.638 10.319 -0.340 -0.652 HAT VBN 71 VBN HAU HAU H 0 1 N N N 26.631 21.951 3.968 -3.050 1.479 0.440 HAU VBN 72 VBN HAUA HAUA H 0 0 N N N 27.292 20.482 4.811 -4.097 0.427 -0.543 HAUA VBN 73 VBN HAV HAV H 0 1 N N N 28.346 19.143 3.471 0.800 0.993 -1.504 HAV VBN 74 VBN HAVA HAVA H 0 0 N N N 27.744 19.081 1.760 1.085 -0.762 -1.419 HAVA VBN 75 VBN HAW HAW H 0 1 N N N 26.000 22.236 6.173 -3.385 3.326 -1.181 HAW VBN 76 VBN HAWA HAWA H 0 0 N N N 24.522 21.535 5.374 -4.432 2.274 -2.163 HAWA VBN 77 VBN HAX HAX H 0 1 N N N 28.803 16.815 1.538 1.966 1.287 0.664 HAX VBN 78 VBN HAXA HAXA H 0 0 N N N 29.984 18.138 1.854 2.251 -0.468 0.749 HAXA VBN 79 VBN HAY HAY H 0 1 N N N 24.647 20.418 3.378 -2.547 0.617 -2.444 HAY VBN 80 VBN HAYA HAYA H 0 0 N N N 26.220 20.247 2.481 -1.520 1.738 -1.519 HAYA VBN 81 VBN HAZ HAZ H 0 1 N N N 26.259 17.302 2.255 -0.214 -0.871 0.691 HAZ VBN 82 VBN HAZA HAZA H 0 0 N N N 27.007 17.047 3.890 -0.499 0.884 0.605 HAZA VBN 83 VBN HNBB HNBB H 0 0 N N N 25.003 19.456 6.572 -5.442 2.322 0.475 HNBB VBN 84 VBN HNBC HNBC H 0 0 N N N 30.309 17.269 4.065 3.276 0.482 -1.705 HNBC VBN 85 VBN HBU HBU H 0 1 N N N 30.791 13.298 4.186 6.105 -1.203 -0.574 HBU VBN 86 VBN HBX HBX H 0 1 N N N 30.265 15.747 5.420 5.546 1.474 -1.900 HBX VBN 87 VBN HG2 HG2 H 0 1 N N N 23.899 14.507 1.656 1.378 -3.379 -0.516 HG2 VBN 88 VBN HG2A HG2A H 0 0 N N N 25.490 15.089 2.251 1.437 -4.081 -2.151 HG2A VBN 89 VBN HG2B HG2B H 0 0 N N N 24.511 13.968 3.256 1.136 -2.340 -1.941 HG2B VBN 90 # # 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 VBN C O DOUB N N 1 VBN C CA SING N N 2 VBN C NBY SING N N 3 VBN N CA SING N N 4 VBN N CBJ DOUB N N 5 VBN CA CB SING N N 6 VBN CB OG1 SING N N 7 VBN CB CG2 SING N N 8 VBN CAB CBU SING N N 9 VBN OAC CBG DOUB N N 10 VBN OAD CBH DOUB N N 11 VBN OAF CBK SING N N 12 VBN OAG CBL SING N N 13 VBN OAH CBM SING N N 14 VBN OAI CBN SING N N 15 VBN OAJ CBO SING N N 16 VBN OAK CBP SING N N 17 VBN CAL CAO DOUB Y N 18 VBN CAL CAR SING Y N 19 VBN CAM CAP DOUB Y N 20 VBN CAM CAS SING Y N 21 VBN CAN CAQ DOUB Y N 22 VBN CAN CAT SING Y N 23 VBN CAO CBK SING Y N 24 VBN CAP CBL SING Y N 25 VBN CAQ CBM SING Y N 26 VBN CAR CBQ DOUB Y N 27 VBN CAS CBR DOUB Y N 28 VBN CAT CBS DOUB Y N 29 VBN CAU CAW SING N N 30 VBN CAU CAY SING N N 31 VBN CAV CAX SING N N 32 VBN CAV CAZ SING N N 33 VBN CAW NBB SING N N 34 VBN CAX NBC SING N N 35 VBN CAY NBY SING N N 36 VBN CAZ NBY SING N N 37 VBN NBB CBG SING N N 38 VBN NBC CBH SING N N 39 VBN NBD CBW DOUB N N 40 VBN NBD CBX SING N N 41 VBN OBF CBU SING N N 42 VBN OBF CBW SING N N 43 VBN CBG CBQ SING N N 44 VBN CBH CBX SING N N 45 VBN CBJ CBR SING N N 46 VBN CBJ OG1 SING N N 47 VBN CBK CBN DOUB Y N 48 VBN CBL CBO DOUB Y N 49 VBN CBM CBP DOUB Y N 50 VBN CBN CBQ SING Y N 51 VBN CBO CBR SING Y N 52 VBN CBP CBS SING Y N 53 VBN CBS CBW SING N N 54 VBN CBU CBX SING N N 55 VBN CA HA SING N N 56 VBN CB HB SING N N 57 VBN CAB HAB SING N N 58 VBN CAB HABA SING N N 59 VBN CAB HABB SING N N 60 VBN OAF HOAF SING N N 61 VBN OAG HOAG SING N N 62 VBN OAH HOAH SING N N 63 VBN OAI HOAI SING N N 64 VBN OAJ HOAJ SING N N 65 VBN OAK HOAK SING N N 66 VBN CAL HAL SING N N 67 VBN CAM HAM SING N N 68 VBN CAN HAN SING N N 69 VBN CAO HAO SING N N 70 VBN CAP HAP SING N N 71 VBN CAQ HAQ SING N N 72 VBN CAR HAR SING N N 73 VBN CAS HAS SING N N 74 VBN CAT HAT SING N N 75 VBN CAU HAU SING N N 76 VBN CAU HAUA SING N N 77 VBN CAV HAV SING N N 78 VBN CAV HAVA SING N N 79 VBN CAW HAW SING N N 80 VBN CAW HAWA SING N N 81 VBN CAX HAX SING N N 82 VBN CAX HAXA SING N N 83 VBN CAY HAY SING N N 84 VBN CAY HAYA SING N N 85 VBN CAZ HAZ SING N N 86 VBN CAZ HAZA SING N N 87 VBN NBB HNBB SING N N 88 VBN NBC HNBC SING N N 89 VBN CBU HBU SING N N 90 VBN CBX HBX SING N N 91 VBN CG2 HG2 SING N N 92 VBN CG2 HG2A SING N N 93 VBN CG2 HG2B SING N N 94 # # 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 VBN SMILES ACDLabs 12.01 "O=C(N(CCCNC(=O)c1cccc(O)c1O)CCCNC(=O)C2N=C(OC2C)c3cccc(O)c3O)C4N=C(OC4C)c5cccc(O)c5O" VBN SMILES_CANONICAL CACTVS 3.370 "C[C@H]1OC(=N[C@@H]1C(=O)NCCCN(CCCNC(=O)c2cccc(O)c2O)C(=O)[C@H]3N=C(O[C@@H]3C)c4cccc(O)c4O)c5cccc(O)c5O" VBN SMILES CACTVS 3.370 "C[CH]1OC(=N[CH]1C(=O)NCCCN(CCCNC(=O)c2cccc(O)c2O)C(=O)[CH]3N=C(O[CH]3C)c4cccc(O)c4O)c5cccc(O)c5O" VBN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@@H]1[C@H](N=C(O1)c2cccc(c2O)O)C(=O)NCCCN(CCCNC(=O)c3cccc(c3O)O)C(=O)[C@@H]4[C@H](OC(=N4)c5cccc(c5O)O)C" VBN SMILES "OpenEye OEToolkits" 1.7.0 "CC1C(N=C(O1)c2cccc(c2O)O)C(=O)NCCCN(CCCNC(=O)c3cccc(c3O)O)C(=O)C4C(OC(=N4)c5cccc(c5O)O)C" VBN InChI InChI 1.03 "InChI=1S/C35H39N5O11/c1-18-26(38-33(50-18)21-9-4-12-24(42)29(21)45)32(48)37-15-7-17-40(16-6-14-36-31(47)20-8-3-11-23(41)28(20)44)35(49)27-19(2)51-34(39-27)22-10-5-13-25(43)30(22)46/h3-5,8-13,18-19,26-27,41-46H,6-7,14-17H2,1-2H3,(H,36,47)(H,37,48)/t18-,19-,26+,27+/m1/s1" VBN InChIKey InChI 1.03 LLMKLMMXMOTPRU-QCOILQKOSA-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 VBN "SYSTEMATIC NAME" ACDLabs 12.01 "(4S,5R)-N-{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-N-[3-({[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide" VBN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(4S,5R)-2-(2,3-dihydroxyphenyl)-N-[3-[(2,3-dihydroxyphenyl)carbonylamino]propyl]-N-[3-[[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]carbonylamino]propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VBN "Create component" 2011-04-06 PDBJ VBN "Modify aromatic_flag" 2011-06-04 RCSB VBN "Modify descriptor" 2011-06-04 RCSB VBN "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VBN _pdbx_chem_comp_synonyms.name vibriobactin _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##