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 ?
##