data_VRB
# 
_chem_comp.id                                    VRB 
_chem_comp.name                                  "Phycoviolobilin, blue light-absorbing form" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H42 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyr
rol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-08-28 
_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                        590.710 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VRB 
_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        4FOF 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
VRB C01  C01  C 0 1 N N N N N N 17.630 63.468 44.239 6.579   -2.055 2.944  C01 VRB 1  
VRB C02  C02  C 0 1 N N N N N N 16.740 64.579 43.672 6.939   -2.687 1.598  C02 VRB 2  
VRB C03  C03  C 0 1 N N N N N N 15.277 64.338 43.973 6.597   -1.729 0.486  C03 VRB 3  
VRB C04  C04  C 0 1 N N N N N N 14.749 64.495 45.183 7.423   -0.867 -0.097 C04 VRB 4  
VRB C05  C05  C 0 1 N N N N N N 15.419 64.917 46.469 8.877   -0.687 0.255  C05 VRB 5  
VRB C06  C06  C 0 1 N N N N N N 13.338 64.140 45.020 6.707   -0.116 -1.134 C06 VRB 6  
VRB O07  O07  O 0 1 N N N N N N 12.564 64.187 45.961 7.201   0.744  -1.838 O07 VRB 7  
VRB N08  N08  N 0 1 N N N N N N 13.009 63.783 43.759 5.424   -0.520 -1.192 N08 VRB 8  
VRB C09  C09  C 0 1 N N R N N N 14.245 63.890 42.963 5.251   -1.572 -0.182 C09 VRB 9  
VRB C10  C10  C 0 1 N N N N N N 14.659 62.580 42.286 4.205   -1.145 0.851  C10 VRB 10 
VRB C11  C11  C 0 1 Y N N N N N 13.545 61.798 41.625 2.854   -1.054 0.189  C11 VRB 11 
VRB C12  C12  C 0 1 Y N N N N N 12.553 62.232 40.780 1.994   -2.076 0.006  C12 VRB 12 
VRB C13  C13  C 0 1 N N N N N N 12.308 63.644 40.308 2.210   -3.510 0.419  C13 VRB 13 
VRB C14  C14  C 0 1 Y N N N N N 11.766 61.132 40.422 0.855   -1.558 -0.642 C14 VRB 14 
VRB C15  C15  C 0 1 Y N N N N N 12.313 60.014 41.062 1.063   -0.239 -0.830 C15 VRB 15 
VRB C16  C16  C 0 1 N N N N N N 11.815 58.535 40.986 0.106   0.721  -1.487 C16 VRB 16 
VRB C17  C17  C 0 1 Y N N N N N 12.876 57.702 40.177 -0.885  1.221  -0.467 C17 VRB 17 
VRB C18  C18  C 0 1 Y N N N N N 12.650 56.886 39.037 -0.690  2.268  0.373  C18 VRB 18 
VRB C19  C19  C 0 1 N N N N N N 11.340 56.655 38.331 0.548   3.124  0.450  C19 VRB 19 
VRB C20  C20  C 0 1 N N N N N N 10.424 55.733 39.133 0.410   4.308  -0.509 C20 VRB 20 
VRB C21  C21  C 0 1 N N N N N N 9.177  55.453 38.335 1.648   5.164  -0.432 C21 VRB 21 
VRB O22  O22  O 0 1 N N N N N N 8.741  54.189 38.232 1.751   6.266  -1.192 O22 VRB 22 
VRB O23  O23  O 0 1 N N N N N N 8.569  56.350 37.794 2.548   4.858  0.314  O23 VRB 23 
VRB C24  C24  C 0 1 Y N N N N N 13.853 56.355 38.680 -1.839  2.414  1.153  C24 VRB 24 
VRB C25  C25  C 0 1 Y N N N N N 14.813 56.854 39.603 -2.727  1.425  0.757  C25 VRB 25 
VRB N26  N26  N 0 1 Y N N N N N 14.178 57.638 40.469 -2.118  0.700  -0.244 N26 VRB 26 
VRB C27  C27  C 0 1 N N N N N N 16.252 56.600 39.724 -4.017  1.202  1.283  C27 VRB 27 
VRB C28  C28  C 0 1 N N N N N N 17.146 56.102 38.798 -4.926  0.436  0.582  C28 VRB 28 
VRB N29  N29  N 0 1 N N N N N N 17.107 56.156 37.403 -4.760  -0.062 -0.708 N29 VRB 29 
VRB C30  C30  C 0 1 N N N N N N 18.214 55.549 36.926 -5.862  -0.763 -1.036 C30 VRB 30 
VRB O31  O31  O 0 1 N N N N N N 18.503 55.409 35.749 -6.052  -1.336 -2.096 O31 VRB 31 
VRB C32  C32  C 0 1 N N N N N N 18.981 55.096 38.017 -6.757  -0.725 0.048  C32 VRB 32 
VRB C33  C33  C 0 1 N N N N N N 18.339 55.441 39.158 -6.187  0.010  1.043  C33 VRB 33 
VRB C34  C34  C 0 1 N N N N N N 18.815 55.155 40.552 -6.791  0.307  2.391  C34 VRB 34 
VRB C35  C35  C 0 1 N N N N N N 20.300 54.382 37.936 -8.112  -1.383 0.100  C35 VRB 35 
VRB C36  C36  C 0 1 N N N N N N 21.355 55.473 37.874 -9.153  -0.459 -0.536 C36 VRB 36 
VRB C37  C37  C 0 1 N N N N N N 14.087 55.427 37.518 -2.070  3.450  2.223  C37 VRB 37 
VRB N38  N38  N 0 1 Y N N N N N 13.402 60.442 41.785 2.288   0.076  -0.322 N38 VRB 38 
VRB C39  C39  C 0 1 N N N N N N 10.559 61.137 39.508 -0.370  -2.335 -1.050 C39 VRB 39 
VRB C40  C40  C 0 1 N N N N N N 9.342  61.776 40.180 -1.388  -2.321 0.092  C40 VRB 40 
VRB C41  C41  C 0 1 N N N N N N 8.655  60.744 41.029 -2.613  -3.098 -0.316 C41 VRB 41 
VRB O42  O42  O 0 1 N N N N N N 8.713  60.812 42.234 -3.644  -3.220 0.534  O42 VRB 42 
VRB O43  O43  O 0 1 N N N N N N 7.984  59.747 40.439 -2.666  -3.610 -1.409 O43 VRB 43 
VRB H1   H1   H 0 1 N N N N N N 18.682 63.682 43.999 5.511   -1.837 2.969  H1  VRB 44 
VRB H2   H2   H 0 1 N N N N N N 17.506 63.420 45.331 6.826   -2.748 3.749  H2  VRB 45 
VRB H3   H3   H 0 1 N N N N N N 17.341 62.504 43.795 7.142   -1.131 3.075  H3  VRB 46 
VRB H4   H4   H 0 1 N N N N N N 16.876 64.622 42.581 8.007   -2.905 1.574  H4  VRB 47 
VRB H5   H5   H 0 1 N N N N N N 17.041 65.538 44.118 6.376   -3.611 1.468  H5  VRB 48 
VRB H6   H6   H 0 1 N N N N N N 14.676 64.941 47.279 9.484   -1.358 -0.354 H6  VRB 49 
VRB H7   H7   H 0 1 N N N N N N 16.213 64.199 46.721 9.173   0.345  0.063  H7  VRB 50 
VRB H8   H8   H 0 1 N N N N N N 15.857 65.918 46.343 9.028   -0.918 1.310  H8  VRB 51 
VRB H9   H9   H 0 1 N N N N N N 12.107 63.502 43.431 4.742   -0.182 -1.792 H9  VRB 52 
VRB H10  H10  H 0 1 N N N N N N 14.127 64.669 42.195 4.950   -2.505 -0.658 H10 VRB 53 
VRB H11  H11  H 0 1 N N N N N N 15.406 62.820 41.515 4.167   -1.879 1.655  H11 VRB 54 
VRB H12  H12  H 0 1 N N N N N N 15.116 61.935 43.051 4.475   -0.171 1.260  H12 VRB 55 
VRB H13  H13  H 0 1 N N N N N N 12.864 63.821 39.375 1.833   -3.657 1.431  H13 VRB 56 
VRB H14  H14  H 0 1 N N N N N N 11.233 63.789 40.127 1.678   -4.169 -0.267 H14 VRB 57 
VRB H15  H15  H 0 1 N N N N N N 12.649 64.352 41.078 3.275   -3.739 0.391  H15 VRB 58 
VRB H16  H16  H 0 1 N N N N N N 11.713 58.123 42.001 0.661   1.564  -1.898 H16 VRB 59 
VRB H17  H17  H 0 1 N N N N N N 10.842 58.495 40.475 -0.426  0.211  -2.290 H17 VRB 60 
VRB H18  H18  H 0 1 N N N N N N 10.836 57.622 38.188 0.671   3.494  1.468  H18 VRB 61 
VRB H19  H19  H 0 1 N N N N N N 11.539 56.197 37.351 1.418   2.530  0.171  H19 VRB 62 
VRB H20  H20  H 0 1 N N N N N N 10.946 54.788 39.342 0.287   3.938  -1.527 H20 VRB 63 
VRB H21  H21  H 0 1 N N N N N N 10.152 56.220 40.081 -0.460  4.902  -0.231 H21 VRB 64 
VRB H22  H22  H 0 1 N N N N N N 7.950  54.168 37.706 2.563   6.783  -1.108 H22 VRB 65 
VRB H23  H23  H 0 1 N N N N N N 14.614 58.114 41.233 -2.508  -0.054 -0.714 H23 VRB 66 
VRB H26  H26  H 0 1 N N N N N N 19.779 54.627 40.510 -6.097  0.914  2.974  H26 VRB 67 
VRB H27  H27  H 0 1 N N N N N N 18.939 56.102 41.098 -7.726  0.850  2.258  H27 VRB 68 
VRB H28  H28  H 0 1 N N N N N N 18.075 54.527 41.070 -6.985  -0.628 2.916  H28 VRB 69 
VRB H29  H29  H 0 1 N N N N N N 20.451 53.753 38.826 -8.080  -2.325 -0.448 H29 VRB 70 
VRB H30  H30  H 0 1 N N N N N N 20.342 53.756 37.033 -8.383  -1.575 1.138  H30 VRB 71 
VRB H31  H31  H 0 1 N N N N N N 22.353 55.015 37.813 -9.185  0.483  0.011  H31 VRB 72 
VRB H32  H32  H 0 1 N N N N N N 21.184 56.099 36.986 -8.882  -0.267 -1.574 H32 VRB 73 
VRB H33  H33  H 0 1 N N N N N N 21.292 56.096 38.779 -10.132 -0.935 -0.499 H33 VRB 74 
VRB H34  H34  H 0 1 N N N N N N 14.318 56.016 36.618 -2.521  4.337  1.778  H34 VRB 75 
VRB H35  H35  H 0 1 N N N N N N 14.932 54.760 37.746 -2.737  3.044  2.983  H35 VRB 76 
VRB H36  H36  H 0 1 N N N N N N 13.183 54.826 37.341 -1.117  3.718  2.681  H36 VRB 77 
VRB H37  H37  H 0 1 N N N N N N 13.995 59.858 42.339 2.689   0.959  -0.320 H37 VRB 78 
VRB H38  H38  H 0 1 N N N N N N 10.313 60.100 39.237 -0.812  -1.878 -1.936 H38 VRB 79 
VRB H39  H39  H 0 1 N N N N N N 10.803 61.705 38.598 -0.090  -3.364 -1.274 H39 VRB 80 
VRB H40  H40  H 0 1 N N N N N N 9.668  62.616 40.811 -0.946  -2.778 0.978  H40 VRB 81 
VRB H41  H41  H 0 1 N N N N N N 8.647  62.144 39.411 -1.668  -1.291 0.316  H41 VRB 82 
VRB H42  H42  H 0 1 N N N N N N 8.233  60.086 42.616 -4.408  -3.728 0.228  H42 VRB 83 
VRB H24  H24  H 0 1 N N N N N N 16.678 56.840 40.687 -4.293  1.631  2.235  H24 VRB 84 
VRB H421 H421 H 0 0 N N N N N N 16.384 56.573 36.852 -3.984  0.074  -1.274 ?   ?   85 
# 
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 
VRB C01 H1   SING N N 1  
VRB C01 H2   SING N N 2  
VRB C01 H3   SING N N 3  
VRB C02 C03  SING N N 4  
VRB C02 C01  SING N N 5  
VRB C02 H4   SING N N 6  
VRB C02 H5   SING N N 7  
VRB C03 C04  DOUB N N 8  
VRB C04 C05  SING N N 9  
VRB C05 H6   SING N N 10 
VRB C05 H7   SING N N 11 
VRB C05 H8   SING N N 12 
VRB C06 C04  SING N N 13 
VRB C06 O07  DOUB N N 14 
VRB N08 C06  SING N N 15 
VRB N08 H9   SING N N 16 
VRB C09 N08  SING N N 17 
VRB C09 C03  SING N N 18 
VRB C09 H10  SING N N 19 
VRB C10 C09  SING N N 20 
VRB C10 H11  SING N N 21 
VRB C10 H12  SING N N 22 
VRB C11 N38  SING Y N 23 
VRB C11 C10  SING N N 24 
VRB C12 C11  DOUB Y N 25 
VRB C13 C12  SING N N 26 
VRB C13 H13  SING N N 27 
VRB C13 H14  SING N N 28 
VRB C13 H15  SING N N 29 
VRB C14 C12  SING Y N 30 
VRB C14 C15  DOUB Y N 31 
VRB C15 N38  SING Y N 32 
VRB C16 C15  SING N N 33 
VRB C16 H16  SING N N 34 
VRB C16 H17  SING N N 35 
VRB C17 N26  SING Y N 36 
VRB C17 C16  SING N N 37 
VRB C18 C17  DOUB Y N 38 
VRB C19 C18  SING N N 39 
VRB C19 C20  SING N N 40 
VRB C19 H18  SING N N 41 
VRB C19 H19  SING N N 42 
VRB C20 H20  SING N N 43 
VRB C20 H21  SING N N 44 
VRB C21 C20  SING N N 45 
VRB O22 C21  SING N N 46 
VRB O22 H22  SING N N 47 
VRB O23 C21  DOUB N N 48 
VRB C24 C18  SING Y N 49 
VRB C24 C25  DOUB Y N 50 
VRB C25 C27  SING N N 51 
VRB C25 N26  SING Y N 52 
VRB N26 H23  SING N N 53 
VRB C28 C33  SING N N 54 
VRB C28 C27  DOUB N Z 55 
VRB N29 C28  SING N N 56 
VRB C30 N29  SING N N 57 
VRB C30 C32  SING N N 58 
VRB O31 C30  DOUB N N 59 
VRB C32 C33  DOUB N N 60 
VRB C33 C34  SING N N 61 
VRB C34 H26  SING N N 62 
VRB C34 H27  SING N N 63 
VRB C34 H28  SING N N 64 
VRB C35 C32  SING N N 65 
VRB C35 H29  SING N N 66 
VRB C35 H30  SING N N 67 
VRB C36 C35  SING N N 68 
VRB C36 H31  SING N N 69 
VRB C36 H32  SING N N 70 
VRB C36 H33  SING N N 71 
VRB C37 C24  SING N N 72 
VRB C37 H34  SING N N 73 
VRB C37 H35  SING N N 74 
VRB C37 H36  SING N N 75 
VRB N38 H37  SING N N 76 
VRB C39 C40  SING N N 77 
VRB C39 C14  SING N N 78 
VRB C39 H38  SING N N 79 
VRB C39 H39  SING N N 80 
VRB C40 C41  SING N N 81 
VRB C40 H40  SING N N 82 
VRB C40 H41  SING N N 83 
VRB C41 O42  SING N N 84 
VRB O42 H42  SING N N 85 
VRB O43 C41  DOUB N N 86 
VRB C27 H24  SING N N 87 
VRB N29 H421 SING N N 88 
# 
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 
VRB InChI            InChI                1.03  "InChI=1S/C33H42N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h13,27,34-35H,7-12,14-15H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-/t27-/m1/s1" 
VRB InChIKey         InChI                1.03  KTSIPBCNIBDFRK-JTNIOKRPSA-N                                                                                                                                                                                                                         
VRB SMILES_CANONICAL CACTVS               3.370 "CCC1=C(C)C(=O)N[C@@H]1Cc2[nH]c(Cc3[nH]c(\C=C4/NC(=O)C(=C4C)CC)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C"                                                                                                                                                       
VRB SMILES           CACTVS               3.370 "CCC1=C(C)C(=O)N[CH]1Cc2[nH]c(Cc3[nH]c(C=C4NC(=O)C(=C4C)CC)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C"                                                                                                                                                           
VRB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCC1=C(C(=O)NC1Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)/C=C\4/C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C"                                                                                                                                                     
VRB SMILES           "OpenEye OEToolkits" 1.7.6 "CCC1=C(C(=O)NC1Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)C=C4C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C"                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           VRB 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   1.7.6 
_pdbx_chem_comp_identifier.identifier        "3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VRB "Create component"   2012-08-28 RCSB 
VRB "Other modification" 2013-05-08 RCSB 
VRB "Modify synonyms"    2020-06-05 PDBE 
VRB "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VRB 
_pdbx_chem_comp_synonyms.name         "3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 VRB CYS None Crosslinker "Amino-acid side chain" "Any position" C02 SG ? ? 
2 VRB CYS None Crosslinker "Amino-acid side chain" "Any position" C16 SG ? ? 
# 
