data_LBV # _chem_comp.id LBV _chem_comp.name ;3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H37 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2(R),3(E)- PHYTOCHROMOBILIN" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2006-12-22 _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 585.670 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LBV _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 2O9B _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 LBV C1A C1A C 0 1 N N N N N N 26.526 -30.390 16.343 3.362 0.819 -2.000 C1A LBV 1 LBV C1B C1B C 0 1 Y N N N N N 22.609 -28.774 17.577 0.250 2.503 0.284 C1B LBV 2 LBV O1B O1B O 0 1 N N N N N N 16.978 -25.147 17.049 -5.895 3.547 1.275 O1B LBV 3 LBV C1C C1C C 0 1 N N N N N N 20.769 -28.319 13.593 -1.752 -1.216 -0.228 C1C LBV 4 LBV O1C O1C O 0 1 N N N N N N 19.877 -24.264 11.275 -7.065 -3.036 0.953 O1C LBV 5 LBV C1D C1D C 0 1 N N N N N N 23.338 -29.581 9.893 2.051 -2.863 0.451 C1D LBV 6 LBV C2A C2A C 0 1 N N S N N N 27.044 -30.796 17.690 4.562 1.528 -1.414 C2A LBV 7 LBV C2B C2B C 0 1 Y N N N N N 21.545 -28.177 18.239 -0.866 3.225 0.720 C2B LBV 8 LBV O2B O2B O 0 1 N N N N N N 18.231 -23.999 18.516 -6.315 4.261 -0.773 O2B LBV 9 LBV C2C C2C C 0 1 N N N N N N 19.997 -28.092 12.442 -2.427 -2.398 -0.615 C2C LBV 10 LBV O2C O2C O 0 1 N N N N N N 18.289 -25.423 10.219 -6.517 -2.790 -1.173 O2C LBV 11 LBV C2D C2D C 0 1 N N N N N N 24.130 -30.546 9.271 3.365 -3.357 0.467 C2D LBV 12 LBV C3A C3A C 0 1 N N N N N N 25.870 -30.334 18.525 3.971 2.513 -0.423 C3A LBV 13 LBV C3B C3B C 0 1 Y N N N N N 20.610 -27.788 17.296 -1.959 2.411 0.634 C3B LBV 14 LBV C3C C3C C 0 1 N N N N N N 20.697 -28.646 11.393 -1.503 -3.396 -0.617 C3C LBV 15 LBV C3D C3D C 0 1 N N N N N N 24.506 -30.044 8.040 4.154 -2.419 1.114 C3D LBV 16 LBV C4A C4A C 0 1 N N N N N N 24.871 -29.786 17.718 2.518 2.303 -0.510 C4A LBV 17 LBV C4B C4B C 0 1 Y N N N N N 21.107 -28.167 16.050 -1.531 1.168 0.141 C4B LBV 18 LBV C4C C4C C 0 1 N N N N N N 21.879 -29.177 11.899 -0.272 -2.817 -0.231 C4C LBV 19 LBV C4D C4D C 0 1 N N N N N N 23.939 -28.791 7.963 3.269 -1.317 1.501 C4D LBV 20 LBV CAA CAA C 0 1 N N N N N N 25.843 -30.471 19.899 4.624 3.377 0.355 CAA LBV 21 LBV CAB CAB C 0 1 N N N N N N 19.281 -27.062 17.597 -3.372 2.780 1.003 CAB LBV 22 LBV CAC CAC C 0 1 N N N N N N 18.643 -27.402 12.282 -3.888 -2.525 -0.959 CAC LBV 23 LBV CAD CAD C 0 1 N N N N N N 25.311 -30.713 7.108 5.603 -2.513 1.365 CAD LBV 24 LBV CBA CBA C 0 1 N N N N N N 26.867 -31.025 20.662 6.121 3.513 0.238 CBA LBV 25 LBV CBB CBB C 0 1 N N N N N N 19.296 -25.605 17.124 -4.084 3.360 -0.220 CBB LBV 26 LBV CBC CBC C 0 1 N N N N N N 18.673 -25.889 12.512 -4.699 -2.725 0.323 CBC LBV 27 LBV CBD CBD C 0 1 N N N N N N 25.690 -30.217 5.862 6.211 -1.589 2.104 CBD LBV 28 LBV CGB CGB C 0 1 N N N N N N 18.063 -24.857 17.607 -5.498 3.730 0.149 CGB LBV 29 LBV CGC CGC C 0 1 N N N N N N 18.969 -25.125 11.224 -6.160 -2.853 -0.021 CGC LBV 30 LBV CHB CHB C 0 1 N N N N N N 23.692 -29.291 18.295 1.571 2.986 0.218 CHB LBV 31 LBV CHC CHC C 0 1 N N N N N N 20.373 -27.893 14.874 -2.333 0.061 -0.095 CHC LBV 32 LBV CHD CHD C 0 1 N N N N N N 22.840 -29.863 11.161 0.960 -3.502 -0.103 CHD LBV 33 LBV CMA CMA C 0 1 N N N N N N 28.292 -29.970 18.019 5.333 2.269 -2.508 CMA LBV 34 LBV CMB CMB C 0 1 N N N N N N 21.415 -27.953 19.750 -0.862 4.653 1.202 CMB LBV 35 LBV CMC CMC C 0 1 N N N N N N 20.221 -28.640 9.926 -1.746 -4.843 -0.964 CMC LBV 36 LBV CMD CMD C 0 1 N N N N N N 24.517 -31.927 9.828 3.832 -4.667 -0.113 CMD LBV 37 LBV N_A N_A N 0 1 N N N N N N 25.304 -29.843 16.444 2.252 1.316 -1.436 N_A LBV 38 LBV O_A O_A O 0 1 N N N N N N 27.158 -30.562 15.297 3.398 -0.051 -2.844 O_A LBV 39 LBV N_B N_B N 0 1 Y N N N N N 22.294 -28.754 16.271 -0.162 1.243 -0.064 N_B LBV 40 LBV N_C N_C N 1 1 N N N N N N 21.863 -28.969 13.210 -0.469 -1.518 -0.005 N_C LBV 41 LBV N_D N_D N 0 1 N N N N N N 23.242 -28.525 9.066 2.024 -1.628 1.090 N_D LBV 42 LBV O_D O_D O 0 1 N N N N N N 24.051 -28.034 7.016 3.598 -0.303 2.092 O_D LBV 43 LBV HO1C HO1C H 0 1 N N N N N N 19.979 -23.859 10.422 -7.991 -3.112 0.684 HO1C LBV 44 LBV H2A H2A H 0 1 N N N N N N 27.334 -31.850 17.815 5.213 0.818 -0.905 H2A LBV 45 LBV HO2B HO2B H 0 1 N N N N N N 17.399 -23.592 18.725 -7.213 4.482 -0.489 HO2B LBV 46 LBV HAA1 HAA1 H 0 1 N N N N N N 24.963 -30.123 20.420 4.081 3.979 1.068 HAA1 LBV 47 LBV HAB1 HAB1 H 0 1 N N N N N N 18.468 -27.590 17.077 -3.903 1.891 1.344 HAB1 LBV 48 LBV HAB2 HAB2 H 0 1 N N N N N N 19.113 -27.075 18.684 -3.357 3.522 1.801 HAB2 LBV 49 LBV HAC1 HAC1 H 0 1 N N N N N N 18.293 -27.580 11.255 -4.224 -1.618 -1.463 HAC1 LBV 50 LBV HAC2 HAC2 H 0 1 N N N N N N 17.952 -27.841 13.016 -4.034 -3.382 -1.618 HAC2 LBV 51 LBV HAD1 HAD1 H 0 1 N N N N N N 25.668 -31.696 7.378 6.172 -3.332 0.950 HAD1 LBV 52 LBV HBA1 HBA1 H 0 1 N N N N N N 26.583 -31.010 21.725 6.372 3.939 -0.733 HBA1 LBV 53 LBV HBA2 HBA2 H 0 1 N N N N N N 27.040 -32.064 20.344 6.488 4.168 1.028 HBA2 LBV 54 LBV HBA3 HBA3 H 0 1 N N N N N N 27.787 -30.440 20.520 6.584 2.531 0.336 HBA3 LBV 55 LBV HBB1 HBB1 H 0 1 N N N N N N 20.193 -25.110 17.524 -3.554 4.249 -0.561 HBB1 LBV 56 LBV HBB2 HBB2 H 0 1 N N N N N N 19.315 -25.588 16.024 -4.099 2.618 -1.018 HBB2 LBV 57 LBV HBC1 HBC1 H 0 1 N N N N N N 17.691 -25.571 12.893 -4.363 -3.632 0.827 HBC1 LBV 58 LBV HBC2 HBC2 H 0 1 N N N N N N 19.459 -25.660 13.247 -4.554 -1.869 0.982 HBC2 LBV 59 LBV HBD1 HBD1 H 0 1 N N N N N N 26.315 -30.811 5.212 7.285 -1.605 2.213 HBD1 LBV 60 LBV HBD2 HBD2 H 0 1 N N N N N N 25.358 -29.239 5.547 5.630 -0.822 2.595 HBD2 LBV 61 LBV HHB1 HHB1 H 0 1 N N N N N N 23.615 -29.311 19.372 1.841 3.892 0.740 HHB1 LBV 62 LBV HHC1 HHC1 H 0 1 N N N N N N 19.458 -27.326 14.963 -3.404 0.178 -0.175 HHC1 LBV 63 LBV HHD1 HHD1 H 0 1 N N N N N N 23.257 -30.736 11.640 1.047 -4.525 -0.439 HHD1 LBV 64 LBV HMA1 HMA1 H 0 1 N N N N N N 28.677 -30.264 19.007 4.672 2.985 -2.997 HMA1 LBV 65 LBV HMA2 HMA2 H 0 1 N N N N N N 29.063 -30.152 17.256 6.176 2.797 -2.064 HMA2 LBV 66 LBV HMA3 HMA3 H 0 1 N N N N N N 28.032 -28.901 18.030 5.699 1.552 -3.243 HMA3 LBV 67 LBV HMB1 HMB1 H 0 1 N N N N N N 21.852 -26.979 20.016 -1.028 5.322 0.357 HMB1 LBV 68 LBV HMB2 HMB2 H 0 1 N N N N N N 20.352 -27.967 20.033 -1.657 4.791 1.935 HMB2 LBV 69 LBV HMB3 HMB3 H 0 1 N N N N N N 21.948 -28.752 20.286 0.100 4.880 1.661 HMB3 LBV 70 LBV HMC1 HMC1 H 0 1 N N N N N N 20.967 -29.147 9.296 -1.590 -4.991 -2.032 HMC1 LBV 71 LBV HMC2 HMC2 H 0 1 N N N N N N 19.258 -29.167 9.851 -1.053 -5.471 -0.405 HMC2 LBV 72 LBV HMC3 HMC3 H 0 1 N N N N N N 20.098 -27.601 9.585 -2.770 -5.111 -0.705 HMC3 LBV 73 LBV HMD1 HMD1 H 0 1 N N N N N N 25.150 -32.453 9.098 4.130 -4.519 -1.151 HMD1 LBV 74 LBV HMD2 HMD2 H 0 1 N N N N N N 25.071 -31.800 10.770 4.683 -5.035 0.460 HMD2 LBV 75 LBV HMD3 HMD3 H 0 1 N N N N N N 23.606 -32.515 10.014 3.021 -5.394 -0.067 HMD3 LBV 76 LBV HAD HAD H 0 1 N N N N N N 24.775 -29.515 15.661 1.357 1.015 -1.656 HAD LBV 77 LBV HAE HAE H 0 1 N N N N N N 22.875 -29.131 15.550 0.403 0.531 -0.401 HAE LBV 78 LBV HAF HAF H 0 1 N N N N N N 22.586 -29.265 13.834 0.215 -0.889 0.273 HAF LBV 79 LBV HAG HAG H 0 1 N N N N N N 22.734 -27.683 9.248 1.237 -1.076 1.214 HAG LBV 80 # 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 LBV C1A N_A SING N N 1 LBV C1A C2A SING N N 2 LBV C1B C2B DOUB Y N 3 LBV C1B CHB SING N N 4 LBV O1B CGB DOUB N N 5 LBV C1C CHC DOUB N Z 6 LBV C1D CHD DOUB N Z 7 LBV C2A CMA SING N N 8 LBV C2A C3A SING N N 9 LBV C2B CMB SING N N 10 LBV C2C C1C SING N N 11 LBV O2C CGC DOUB N N 12 LBV C2D C1D SING N N 13 LBV C2D CMD SING N N 14 LBV C3A CAA DOUB N E 15 LBV C3B C2B SING Y N 16 LBV C3B CAB SING N N 17 LBV C3C C2C DOUB N N 18 LBV C3C C4C SING N N 19 LBV C3D C2D DOUB N N 20 LBV C4A C3A SING N N 21 LBV C4A CHB DOUB N Z 22 LBV C4B C3B DOUB Y N 23 LBV C4B N_B SING Y N 24 LBV C4C N_C DOUB N N 25 LBV C4D C3D SING N N 26 LBV C4D N_D SING N N 27 LBV CAA CBA SING N N 28 LBV CAC C2C SING N N 29 LBV CAC CBC SING N N 30 LBV CAD C3D SING N N 31 LBV CBB CAB SING N N 32 LBV CBB CGB SING N N 33 LBV CBD CAD DOUB N N 34 LBV CGB O2B SING N N 35 LBV CGC O1C SING N N 36 LBV CGC CBC SING N N 37 LBV CHC C4B SING N N 38 LBV CHD C4C SING N N 39 LBV CMC C3C SING N N 40 LBV N_A C4A SING N N 41 LBV O_A C1A DOUB N N 42 LBV N_B C1B SING Y N 43 LBV N_C C1C SING N N 44 LBV N_D C1D SING N N 45 LBV O_D C4D DOUB N N 46 LBV O1C HO1C SING N N 47 LBV C2A H2A SING N N 48 LBV O2B HO2B SING N N 49 LBV CAA HAA1 SING N N 50 LBV CAB HAB1 SING N N 51 LBV CAB HAB2 SING N N 52 LBV CAC HAC1 SING N N 53 LBV CAC HAC2 SING N N 54 LBV CAD HAD1 SING N N 55 LBV CBA HBA1 SING N N 56 LBV CBA HBA2 SING N N 57 LBV CBA HBA3 SING N N 58 LBV CBB HBB1 SING N N 59 LBV CBB HBB2 SING N N 60 LBV CBC HBC1 SING N N 61 LBV CBC HBC2 SING N N 62 LBV CBD HBD1 SING N N 63 LBV CBD HBD2 SING N N 64 LBV CHB HHB1 SING N N 65 LBV CHC HHC1 SING N N 66 LBV CHD HHD1 SING N N 67 LBV CMA HMA1 SING N N 68 LBV CMA HMA2 SING N N 69 LBV CMA HMA3 SING N N 70 LBV CMB HMB1 SING N N 71 LBV CMB HMB2 SING N N 72 LBV CMB HMB3 SING N N 73 LBV CMC HMC1 SING N N 74 LBV CMC HMC2 SING N N 75 LBV CMC HMC3 SING N N 76 LBV CMD HMD1 SING N N 77 LBV CMD HMD2 SING N N 78 LBV CMD HMD3 SING N N 79 LBV N_A HAD SING N N 80 LBV N_B HAE SING N N 81 LBV N_C HAF SING N N 82 LBV N_D HAG SING N N 83 # 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 LBV InChI InChI 1.03 "InChI=1S/C33H36N4O6/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/h7-8,13-15,19,35H,2,9-12H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p+1/b20-7+,26-13-,27-14-,28-15-/t19-/m0/s1" LBV InChIKey InChI 1.03 DKMLMZVDTGOEGU-ISEYCTJISA-O LBV SMILES_CANONICAL CACTVS 3.370 "C/C=C/1[C@H](C)C(=O)NC/1=C/c2[nH]c(/C=C/3[NH+]=C(/C=C/4NC(=O)C(=C/4C)C=C)C(=C/3CCC(O)=O)C)c(CCC(O)=O)c2C" LBV SMILES CACTVS 3.370 "CC=C1[CH](C)C(=O)NC1=Cc2[nH]c(C=C3[NH+]=C(C=C4NC(=O)C(=C4C)C=C)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C" LBV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C/C=C/1\C(C(=O)N\C1=C/c2c(c(c([nH]2)/C=C\3/C(=C(C(=[NH+]3)/C=C\4/C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)C" LBV SMILES "OpenEye OEToolkits" 1.7.2 "CC=C1C(C(=O)NC1=Cc2c(c(c([nH]2)C=C3C(=C(C(=[NH+]3)C=C4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)C" # _pdbx_chem_comp_identifier.comp_id LBV _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.2 _pdbx_chem_comp_identifier.identifier "3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]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 LBV "Create component" 2006-12-22 EBI LBV "Modify descriptor" 2011-06-04 RCSB LBV "Other modification" 2011-07-20 RCSB LBV "Other modification" 2011-09-21 RCSB LBV "Modify synonyms" 2020-06-05 PDBE LBV "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id LBV _pdbx_chem_comp_synonyms.name "2(R),3(E)- PHYTOCHROMOBILIN" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id LBV _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _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 CBA _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #