data_EL5
# 
_chem_comp.id                                    EL5 
_chem_comp.name                                  "3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H36 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "biliverdin, bound form at Pfr state" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-03-26 
_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                        584.662 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     EL5 
_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        6G1Y 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
EL5 C1A C1  C 0 1 N N N N N N 24.739 148.672 20.621 3.708  0.534  1.505  C1A EL5 1  
EL5 C1B C2  C 0 1 N N N N N N 26.599 145.345 22.834 0.363  2.840  0.350  C1B EL5 2  
EL5 O1B O1  O 0 1 N N N N N N 27.920 141.759 27.713 -5.650 3.236  -3.016 O1B EL5 3  
EL5 C1C C3  C 0 1 Y N N N N N 22.719 143.274 22.737 -1.558 -0.852 0.836  C1C EL5 4  
EL5 O1C O2  O 0 1 N N N N N N 18.987 140.472 23.889 -6.288 -2.455 1.842  O1C EL5 5  
EL5 C1D C4  C 0 1 N N N N N N 19.242 145.407 20.713 2.015  -3.071 -0.109 C1D EL5 6  
EL5 C2A C5  C 0 1 N N S N N N 25.897 149.320 20.188 4.822  1.554  1.454  C2A EL5 7  
EL5 C2B C6  C 0 1 N N N N N N 27.305 144.520 23.651 -0.771 3.645  0.073  C2B EL5 8  
EL5 O2B O3  O 0 1 N N N N N N 25.966 140.800 27.690 -5.755 3.823  -0.888 O2B EL5 9  
EL5 C2C C7  C 0 1 Y N N N N N 21.703 142.216 22.458 -2.200 -1.995 1.318  C2C EL5 10 
EL5 O2C O4  O 0 1 N N N N N N 19.538 141.154 25.794 -6.760 -3.107 -0.216 O2C EL5 11 
EL5 C2D C8  C 0 1 N N N N N N 17.900 145.091 21.583 1.667  -2.464 -1.329 C2D EL5 12 
EL5 C3A C9  C 0 1 N N N N N N 26.939 148.646 20.686 4.148  2.831  0.992  C3A EL5 13 
EL5 C3B C10 C 0 1 N N N N N N 26.419 143.531 24.044 -1.857 2.831  0.119  C3B EL5 14 
EL5 C3C C11 C 0 1 Y N N N N N 20.823 142.795 21.674 -1.248 -2.989 1.441  C3C EL5 15 
EL5 C3D C12 C 0 1 N N N N N N 16.958 145.719 20.941 2.746  -2.603 -2.185 C3D EL5 16 
EL5 C4A C13 C 0 1 N N N N N N 26.431 147.502 21.441 2.734  2.464  0.815  C4A EL5 17 
EL5 C4B C14 C 0 1 N N N N N N 25.131 143.806 23.322 -1.380 1.529  0.426  C4B EL5 18 
EL5 C4C C15 C 0 1 Y N N N N N 21.288 144.244 21.520 -0.024 -2.459 1.036  C4C EL5 19 
EL5 C4D C16 C 0 1 N N N N N N 17.563 146.377 19.745 3.785  -3.327 -1.439 C4D EL5 20 
EL5 CAA C17 C 0 1 N N N N N N 28.455 148.921 20.527 4.711  4.022  0.791  CAA EL5 21 
EL5 CAB C18 C 0 1 N N N N N N 26.707 142.403 24.989 -3.291 3.233  -0.110 CAB EL5 22 
EL5 CAC C19 C 0 1 N N N N N N 21.668 140.763 22.945 -3.666 -2.120 1.645  CAC EL5 23 
EL5 CAD C20 C 0 1 N N N N N N 15.497 145.679 21.336 2.835  -2.120 -3.573 CAD EL5 24 
EL5 CBA C21 C 0 1 N N N N N N 29.096 150.143 19.743 6.201  4.186  0.947  CBA EL5 25 
EL5 CBB C22 C 0 1 N N N N N N 26.207 142.715 26.334 -3.666 2.974  -1.571 CBB EL5 26 
EL5 CBC C23 C 0 1 N N N N N N 21.371 140.670 24.402 -4.428 -2.585 0.402  CBC EL5 27 
EL5 CBD C24 C 0 1 N N N N N N 14.470 145.855 20.368 3.901  -2.414 -4.312 CBD EL5 28 
EL5 CGB C25 C 0 1 N N N N N N 26.728 141.686 27.315 -5.100 3.375  -1.800 CGB EL5 29 
EL5 CGC C26 C 0 1 N N N N N N 19.842 140.781 24.722 -5.893 -2.711 0.729  CGC EL5 30 
EL5 CHB C27 C 0 1 N N N N N N 27.159 146.563 22.079 1.747  3.307  0.404  CHB EL5 31 
EL5 CHC C28 C 0 1 N N N N N N 23.834 143.147 23.370 -2.165 0.383  0.569  CHC EL5 32 
EL5 CHD C29 C 0 1 N N N N N N 20.613 145.176 20.651 1.206  -3.146 1.009  CHD EL5 33 
EL5 CMA C30 C 0 1 N N N N N N 25.928 150.768 19.712 5.895  1.123  0.452  CMA EL5 34 
EL5 CMB C31 C 0 1 N N N N N N 28.780 144.700 24.112 -0.771 5.123  -0.218 CMB EL5 35 
EL5 CMC C32 C 0 1 N N N N N N 19.604 142.159 21.095 -1.490 -4.395 1.928  CMC EL5 36 
EL5 CMD C33 C 0 1 N N N N N N 17.777 144.312 22.809 0.359  -1.786 -1.647 CMD EL5 37 
EL5 NA  N1  N 0 1 N N N N N N 25.038 147.493 21.416 2.564  1.127  1.130  NA  EL5 38 
EL5 OA  O5  O 0 1 N N N N N N 23.604 149.032 20.354 3.828  -0.629 1.827  OA  EL5 39 
EL5 NB  N2  N 0 1 N N N N N N 25.335 144.932 22.578 -0.044 1.592  0.558  NB  EL5 40 
EL5 NC  N3  N 0 1 Y N N N N N 22.451 144.467 22.077 -0.223 -1.150 0.673  NC  EL5 41 
EL5 ND  N4  N 0 1 N N N N N N 18.820 146.244 19.603 3.299  -3.588 -0.210 ND  EL5 42 
EL5 OD  O6  O 0 1 N N N N N N 16.944 147.025 19.006 4.885  -3.639 -1.858 OD  EL5 43 
EL5 H1  H1  H 0 1 N N N N N N 28.098 141.046 28.315 -6.573 3.507  -3.115 H1  EL5 44 
EL5 H2  H2  H 0 1 N N N N N N 25.921 148.871 19.184 5.258  1.691  2.444  H2  EL5 45 
EL5 H3  H3  H 0 1 N N N N N N 18.591 141.164 25.870 -7.690 -3.173 0.041  H3  EL5 46 
EL5 H4  H4  H 0 1 N N N N N N 29.135 148.221 20.990 4.100  4.869  0.516  H4  EL5 47 
EL5 H6  H6  H 0 1 N N N N N N 26.214 141.490 24.623 -3.941 2.648  0.541  H6  EL5 48 
EL5 H7  H7  H 0 1 N N N N N N 27.794 142.240 25.036 -3.412 4.293  0.114  H7  EL5 49 
EL5 H8  H8  H 0 1 N N N N N N 20.890 140.221 22.388 -3.799 -2.848 2.445  H8  EL5 50 
EL5 H9  H9  H 0 1 N N N N N N 22.647 140.300 22.752 -4.051 -1.153 1.966  H9  EL5 51 
EL5 H10 H10 H 0 1 N N N N N N 15.230 145.514 22.370 2.035  -1.526 -3.991 H10 EL5 52 
EL5 H12 H12 H 0 1 N N N N N N 30.193 150.080 19.798 6.462  5.240  0.851  H12 EL5 53 
EL5 H13 H13 H 0 1 N N N N N N 28.779 150.110 18.690 6.506  3.824  1.928  H13 EL5 54 
EL5 H14 H14 H 0 1 N N N N N N 28.760 151.087 20.197 6.713  3.614  0.172  H14 EL5 55 
EL5 H15 H15 H 0 1 N N N N N N 26.555 143.715 26.632 -3.016 3.559  -2.222 H15 EL5 56 
EL5 H16 H16 H 0 1 N N N N N N 25.107 142.695 26.331 -3.545 1.914  -1.794 H16 EL5 57 
EL5 H17 H17 H 0 1 N N N N N N 21.738 139.702 24.774 -4.295 -1.858 -0.399 H17 EL5 58 
EL5 H18 H18 H 0 1 N N N N N N 21.898 141.485 24.920 -4.043 -3.553 0.081  H18 EL5 59 
EL5 H19 H19 H 0 1 N N N N N N 13.433 145.823 20.669 3.930  -2.131 -5.354 H19 EL5 60 
EL5 H20 H20 H 0 1 N N N N N N 14.727 146.020 19.332 4.738  -2.935 -3.871 H20 EL5 61 
EL5 H22 H22 H 0 1 N N N N N N 28.233 146.676 22.058 1.987  4.320  0.119  H22 EL5 62 
EL5 H24 H24 H 0 1 N N N N N N 23.798 142.365 24.114 -3.239 0.448  0.475  H24 EL5 63 
EL5 H26 H26 H 0 1 N N N N N N 21.196 145.718 19.921 1.516  -3.731 1.862  H26 EL5 64 
EL5 H28 H28 H 0 1 N N N N N N 26.955 151.039 19.427 5.450  1.028  -0.538 H28 EL5 65 
EL5 H29 H29 H 0 1 N N N N N N 25.264 150.882 18.843 6.687  1.871  0.424  H29 EL5 66 
EL5 H30 H30 H 0 1 N N N N N N 25.587 151.428 20.523 6.312  0.163  0.756  H30 EL5 67 
EL5 H31 H31 H 0 1 N N N N N N 29.064 143.865 24.770 0.252  5.500  -0.185 H31 EL5 68 
EL5 H32 H32 H 0 1 N N N N N N 29.440 144.714 23.232 -1.191 5.299  -1.209 H32 EL5 69 
EL5 H33 H33 H 0 1 N N N N N N 28.880 145.649 24.660 -1.373 5.641  0.529  H33 EL5 70 
EL5 H34 H34 H 0 1 N N N N N N 19.847 141.724 20.114 -1.738 -5.035 1.081  H34 EL5 71 
EL5 H35 H35 H 0 1 N N N N N N 19.249 141.366 21.770 -0.591 -4.771 2.416  H35 EL5 72 
EL5 H36 H36 H 0 1 N N N N N N 18.817 142.918 20.974 -2.317 -4.397 2.638  H36 EL5 73 
EL5 H37 H37 H 0 1 N N N N N N 16.726 144.299 23.132 0.420  -0.733 -1.374 H37 EL5 74 
EL5 H38 H38 H 0 1 N N N N N N 18.116 143.282 22.624 0.154  -1.874 -2.714 H38 EL5 75 
EL5 H39 H39 H 0 1 N N N N N N 18.397 144.767 23.596 -0.443 -2.262 -1.083 H39 EL5 76 
EL5 H40 H40 H 0 1 N N N N N N 24.406 146.842 21.837 1.711  0.668  1.085  H40 EL5 77 
EL5 H42 H42 H 0 1 N N N N N N 23.011 145.295 22.037 0.459  -0.541 0.350  H42 EL5 78 
EL5 H5  H5  H 0 1 N N N N N N 19.394 146.632 18.882 3.773  -4.057 0.494  H5  EL5 79 
# 
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 
EL5 OD  C4D DOUB N N 1  
EL5 ND  C4D SING N N 2  
EL5 ND  C1D SING N N 3  
EL5 CMA C2A SING N N 4  
EL5 CBA CAA SING N N 5  
EL5 C4D C3D SING N N 6  
EL5 C2A C1A SING N N 7  
EL5 C2A C3A SING N N 8  
EL5 OA  C1A DOUB N N 9  
EL5 CBD CAD DOUB N N 10 
EL5 CAA C3A DOUB N E 11 
EL5 C1A NA  SING N N 12 
EL5 CHD C1D DOUB N E 13 
EL5 CHD C4C SING N N 14 
EL5 C3A C4A SING N N 15 
EL5 C1D C2D SING N N 16 
EL5 C3D CAD SING N N 17 
EL5 C3D C2D DOUB N N 18 
EL5 CMC C3C SING N N 19 
EL5 NA  C4A SING N N 20 
EL5 C4A CHB DOUB N Z 21 
EL5 C4C C3C DOUB Y N 22 
EL5 C4C NC  SING Y N 23 
EL5 C2D CMD SING N N 24 
EL5 C3C C2C SING Y N 25 
EL5 NC  C1C SING Y N 26 
EL5 CHB C1B SING N N 27 
EL5 C2C C1C DOUB Y N 28 
EL5 C2C CAC SING N N 29 
EL5 NB  C1B DOUB N N 30 
EL5 NB  C4B SING N N 31 
EL5 C1C CHC SING N N 32 
EL5 C1B C2B SING N N 33 
EL5 CAC CBC SING N N 34 
EL5 C4B CHC DOUB N Z 35 
EL5 C4B C3B SING N N 36 
EL5 C2B C3B DOUB N N 37 
EL5 C2B CMB SING N N 38 
EL5 O1C CGC DOUB N N 39 
EL5 C3B CAB SING N N 40 
EL5 CBC CGC SING N N 41 
EL5 CGC O2C SING N N 42 
EL5 CAB CBB SING N N 43 
EL5 CBB CGB SING N N 44 
EL5 CGB O2B DOUB N N 45 
EL5 CGB O1B SING N N 46 
EL5 O1B H1  SING N N 47 
EL5 C2A H2  SING N N 48 
EL5 O2C H3  SING N N 49 
EL5 CAA H4  SING N N 50 
EL5 CAB H6  SING N N 51 
EL5 CAB H7  SING N N 52 
EL5 CAC H8  SING N N 53 
EL5 CAC H9  SING N N 54 
EL5 CAD H10 SING N N 55 
EL5 CBA H12 SING N N 56 
EL5 CBA H13 SING N N 57 
EL5 CBA H14 SING N N 58 
EL5 CBB H15 SING N N 59 
EL5 CBB H16 SING N N 60 
EL5 CBC H17 SING N N 61 
EL5 CBC H18 SING N N 62 
EL5 CBD H19 SING N N 63 
EL5 CBD H20 SING N N 64 
EL5 CHB H22 SING N N 65 
EL5 CHC H24 SING N N 66 
EL5 CHD H26 SING N N 67 
EL5 CMA H28 SING N N 68 
EL5 CMA H29 SING N N 69 
EL5 CMA H30 SING N N 70 
EL5 CMB H31 SING N N 71 
EL5 CMB H32 SING N N 72 
EL5 CMB H33 SING N N 73 
EL5 CMC H34 SING N N 74 
EL5 CMC H35 SING N N 75 
EL5 CMC H36 SING N N 76 
EL5 CMD H37 SING N N 77 
EL5 CMD H38 SING N N 78 
EL5 CMD H39 SING N N 79 
EL5 NA  H40 SING N N 80 
EL5 NC  H42 SING N N 81 
EL5 ND  H5  SING N N 82 
# 
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 
EL5 SMILES           ACDLabs              12.01 "C\C=C1C(=C/C2=N/C(=C\c3[NH]c(/C=C4/NC(=O)C(C=C)=C4C)c(C)c3CCC(=O)O)C(CCC(=O)O)=C2C)/NC(=O)C1C"                                                                                                                                                                           
EL5 InChI            InChI                1.06  "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/h7-8,13-15,19,34H,2,9-12H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b20-7+,26-13+,27-14-,29-15-/t19-/m0/s1" 
EL5 InChIKey         InChI                1.06  SNHIGJASYQUMKZ-IDFYGOSVSA-N                                                                                                                                                                                                                                               
EL5 SMILES_CANONICAL CACTVS               3.385 "C\C=C\1[C@H](C)C(=O)NC\1=C\C2=NC(=C\c3[nH]c(\C=C/4NC(=O)C(=C/4C)C=C)c(C)c3CCC(O)=O)/C(=C2C)CCC(O)=O"                                                                                                                                                                     
EL5 SMILES           CACTVS               3.385 "CC=C1[CH](C)C(=O)NC1=CC2=NC(=Cc3[nH]c(C=C4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O"                                                                                                                                                                               
EL5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C/C=C/1\[C@@H](C(=O)N\C1=C/C2=N/C(=C\c3c(c(c([nH]3)/C=C/4\C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)/C(=C2C)CCC(=O)O)C"                                                                                                                                                              
EL5 SMILES           "OpenEye OEToolkits" 2.0.7 "CC=C1C(C(=O)NC1=CC2=NC(=Cc3c(c(c([nH]3)C=C4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)C(=C2C)CCC(=O)O)C"                                                                                                                                                                              
# 
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 
EL5 "SYSTEMATIC NAME" ACDLabs              12.01 "3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid"                            
EL5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[5-[(~{E})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[5-[(~{Z})-[(3~{E},4~{S})-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-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 
EL5 "Create component" 2018-03-26 EBI  
EL5 "Initial release"  2018-11-28 RCSB 
EL5 "Modify name"      2023-05-14 RCSB 
EL5 "Modify synonyms"  2024-01-23 PDBE 
EL5 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      EL5 
_pdbx_chem_comp_synonyms.name         "biliverdin, bound form at Pfr state" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            EL5 
_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      ? 
# 
