data_AX9 # _chem_comp.id AX9 _chem_comp.name "DiCys-(15,16)-Dihydrobiliverdin" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H40 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "15,16-DIHYDROBILIVERDIN (double Cys bound form); 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{[(2R)-4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-11-11 _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 588.694 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AX9 _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 7SSF _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 AX9 NB N1 N 0 1 Y N N N N N 12.039 7.146 33.580 -0.260 -1.363 0.035 NB AX9 1 AX9 ND N2 N 0 1 N N N N N N 17.646 9.695 35.902 2.011 1.941 -1.362 ND AX9 2 AX9 OD O1 O 0 1 N N N N N N 19.428 10.910 36.776 3.116 2.223 -3.329 OD AX9 3 AX9 C1A C1 C 0 1 N N N N N N 10.757 6.211 28.200 3.316 -1.497 2.037 C1A AX9 4 AX9 C1B C2 C 0 1 Y N N N N N 11.239 6.718 32.576 0.057 -2.621 -0.401 C1B AX9 5 AX9 C1C C3 C 0 1 N N N N N N 13.137 8.449 36.199 -1.638 1.193 0.424 C1C AX9 6 AX9 C1D C4 C 0 1 N N R N N N 17.504 8.422 35.277 2.356 2.223 0.038 C1D AX9 7 AX9 C2A C5 C 0 1 N N N N N N 11.713 5.188 28.073 4.302 -2.287 1.400 C2A AX9 8 AX9 C2B C6 C 0 1 Y N N N N N 9.959 7.227 32.805 -1.103 -3.223 -0.883 C2B AX9 9 AX9 C2C C7 C 0 1 N N N N N N 13.588 9.006 37.415 -2.216 2.405 0.870 C2C AX9 10 AX9 C2D C8 C 0 1 N N N N N N 18.931 7.938 35.154 3.746 2.817 0.008 C2D AX9 11 AX9 C3A C9 C 0 1 N N N N N N 12.220 4.911 29.317 3.695 -3.017 0.432 C3A AX9 12 AX9 C3B C10 C 0 1 Y N N N N N 10.019 7.967 33.943 -2.138 -2.317 -0.738 C3B AX9 13 AX9 C3C C11 C 0 1 N N N N N N 14.920 8.746 37.532 -1.189 3.295 1.000 C3C AX9 14 AX9 C3D C12 C 0 1 N N N N N N 19.773 8.783 35.755 4.124 2.857 -1.266 C3D AX9 15 AX9 C4A C13 C 0 1 N N N N N N 11.566 5.756 30.212 2.316 -2.689 0.456 C4A AX9 16 AX9 C4B C14 C 0 1 Y N N N N N 11.310 7.907 34.438 -1.608 -1.159 -0.165 C4B AX9 17 AX9 C4C C15 C 0 1 N N N N N N 15.328 8.023 36.422 -0.016 2.626 0.638 C4C AX9 18 AX9 C4D C16 C 0 1 N N N N N N 18.986 9.902 36.209 3.060 2.318 -2.118 C4D AX9 19 AX9 CAA C17 C 0 1 N N N N N N 13.325 3.929 29.750 4.363 -3.997 -0.498 CAA AX9 20 AX9 CAB C18 C 0 1 N N N N N N 8.865 8.715 34.579 -3.577 -2.540 -1.127 CAB AX9 21 AX9 CAC C19 C 0 1 N N N N N N 12.753 9.791 38.438 -3.675 2.662 1.146 CAC AX9 22 AX9 CAD C20 C 0 1 N N N N N N 21.274 8.634 35.905 5.449 3.379 -1.760 CAD AX9 23 AX9 CBA C21 C 0 1 N N N N N N 13.490 2.606 29.018 4.243 -5.409 0.077 CBA AX9 24 AX9 CBB C22 C 0 1 N N N N N N 8.388 9.859 33.685 -4.339 -3.140 0.057 CBB AX9 25 AX9 CBC C23 C 0 1 N N N N N N 12.597 9.127 39.797 -4.381 3.044 -0.156 CBC AX9 26 AX9 CBD C24 C 0 1 N N N N N N 21.896 9.519 34.848 6.429 2.215 -1.919 CBD AX9 27 AX9 CGB C25 C 0 1 N N N N N N 9.472 10.867 33.364 -5.778 -3.362 -0.333 CGB AX9 28 AX9 CGC C26 C 0 1 N N N N N N 11.826 10.033 40.766 -5.840 3.301 0.120 CGC AX9 29 AX9 CHA C27 C 0 1 N N N N N N 11.833 5.805 31.534 1.343 -3.209 -0.368 CHA AX9 30 AX9 CHB C28 C 0 1 N N N N N N 11.852 8.536 35.698 -2.323 0.003 0.155 CHB AX9 31 AX9 CHC C29 C 0 1 N N N N N N 16.720 7.515 36.133 1.367 3.227 0.633 CHC AX9 32 AX9 CMA C30 C 0 1 N N N N N N 12.096 4.555 26.755 5.771 -2.312 1.737 CMA AX9 33 AX9 CMB C31 C 0 1 N N N N N N 8.711 7.014 31.969 -1.211 -4.611 -1.459 CMB AX9 34 AX9 CMC C32 C 0 1 N N N N N N 15.800 9.154 38.697 -1.299 4.729 1.451 CMC AX9 35 AX9 CMD C33 C 0 1 N N N N N N 19.296 6.610 34.512 4.549 3.277 1.197 CMD AX9 36 AX9 NA N3 N 0 1 N N N N N N 10.676 6.510 29.529 2.125 -1.748 1.460 NA AX9 37 AX9 NC N4 N 0 1 N N N N N N 14.236 7.851 35.620 -0.311 1.392 0.297 NC AX9 38 AX9 O1B O2 O 0 1 N N N N N N 9.871 10.995 32.171 -6.155 -3.071 -1.443 O1B AX9 39 AX9 O1C O3 O 0 1 N N N N N N 11.915 9.937 42.034 -6.661 3.653 -0.882 O1C AX9 40 AX9 O2B O4 O 0 1 N N N N N N 9.982 11.592 34.282 -6.640 -3.885 0.554 O2B AX9 41 AX9 O2C O5 O 0 1 N N N N N N 11.076 10.918 40.297 -6.271 3.190 1.243 O2C AX9 42 AX9 OA O6 O 0 1 N N N N N N 10.084 6.768 27.326 3.510 -0.723 2.957 OA AX9 43 AX9 HNB H1 H 0 1 N N N N N N 13.012 6.936 33.675 0.358 -0.724 0.423 HNB AX9 44 AX9 HND H2 H 0 1 N N N N N N 16.902 10.336 36.089 1.183 1.551 -1.682 HND AX9 45 AX9 H1D1 H3 H 0 0 N N N N N N 17.046 8.511 34.281 2.353 1.302 0.619 H1D1 AX9 46 AX9 HAA1 H4 H 0 0 N N N N N N 13.140 3.687 30.807 3.878 -3.960 -1.474 HAA1 AX9 47 AX9 HAA2 H5 H 0 0 N N N N N N 14.281 4.465 29.658 5.416 -3.736 -0.605 HAA2 AX9 48 AX9 HAB2 H6 H 0 0 N N N N N N 9.193 9.127 35.545 -4.030 -1.588 -1.405 HAB2 AX9 49 AX9 HAB1 H7 H 0 0 N N N N N N 8.031 8.016 34.743 -3.623 -3.225 -1.973 HAB1 AX9 50 AX9 HAC1 H8 H 0 0 N N N N N N 13.234 10.768 38.591 -4.131 1.761 1.556 HAC1 AX9 51 AX9 HAC2 H9 H 0 0 N N N N N N 11.748 9.939 38.015 -3.770 3.477 1.864 HAC2 AX9 52 AX9 HAD2 H10 H 0 0 N N N N N N 21.570 7.586 35.747 5.310 3.871 -2.722 HAD2 AX9 53 AX9 HAD1 H11 H 0 0 N N N N N N 21.591 8.958 36.907 5.849 4.095 -1.041 HAD1 AX9 54 AX9 HBA3 H12 H 0 0 N N N N N N 14.323 2.041 29.463 4.726 -6.118 -0.595 HBA3 AX9 55 AX9 HBA2 H13 H 0 0 N N N N N N 12.563 2.021 29.105 4.728 -5.446 1.053 HBA2 AX9 56 AX9 HBA1 H14 H 0 0 N N N N N N 13.704 2.799 27.956 3.190 -5.670 0.184 HBA1 AX9 57 AX9 HBB2 H15 H 0 0 N N N N N N 7.567 10.382 34.197 -3.886 -4.092 0.335 HBB2 AX9 58 AX9 HBB1 H16 H 0 0 N N N N N N 8.019 9.432 32.741 -4.293 -2.455 0.903 HBB1 AX9 59 AX9 HBC1 H17 H 0 0 N N N N N N 12.048 8.182 39.675 -3.924 3.944 -0.567 HBC1 AX9 60 AX9 HBC2 H18 H 0 0 N N N N N N 13.594 8.921 40.213 -4.285 2.229 -0.874 HBC2 AX9 61 AX9 HBD3 H19 H 0 0 N N N N N N 22.992 9.450 34.910 7.387 2.592 -2.276 HBD3 AX9 62 AX9 HBD2 H20 H 0 0 N N N N N N 21.564 9.190 33.852 6.568 1.723 -0.956 HBD2 AX9 63 AX9 HBD1 H21 H 0 0 N N N N N N 21.584 10.561 35.012 6.029 1.499 -2.637 HBD1 AX9 64 AX9 HHA1 H22 H 0 0 N N N N N N 12.567 5.099 31.892 1.561 -4.066 -0.988 HHA1 AX9 65 AX9 HHB1 H23 H 0 0 N N N N N N 11.154 9.123 36.276 -3.402 -0.020 0.195 HHB1 AX9 66 AX9 HHC2 H25 H 0 0 N N N N N N 16.639 6.541 35.628 1.662 3.466 1.654 HHC2 AX9 67 AX9 HHC1 H26 H 0 0 N N N N N N 17.251 7.390 37.088 1.365 4.136 0.032 HHC1 AX9 68 AX9 HMA2 H27 H 0 0 N N N N N N 12.862 3.784 26.927 5.967 -1.622 2.557 HMA2 AX9 69 AX9 HMA1 H28 H 0 0 N N N N N N 11.208 4.094 26.298 6.059 -3.320 2.034 HMA1 AX9 70 AX9 HMA3 H29 H 0 0 N N N N N N 12.497 5.326 26.081 6.349 -2.011 0.863 HMA3 AX9 71 AX9 HMB1 H30 H 0 0 N N N N N N 8.177 6.122 32.327 -1.432 -5.320 -0.662 HMB1 AX9 72 AX9 HMB3 H31 H 0 0 N N N N N N 8.056 7.893 32.057 -2.010 -4.636 -2.200 HMB3 AX9 73 AX9 HMB2 H32 H 0 0 N N N N N N 8.995 6.873 30.916 -0.267 -4.881 -1.934 HMB2 AX9 74 AX9 HMC2 H33 H 0 0 N N N N N N 15.203 9.718 39.428 -1.193 4.778 2.534 HMC2 AX9 75 AX9 HMC1 H34 H 0 0 N N N N N N 16.213 8.255 39.177 -0.512 5.318 0.981 HMC1 AX9 76 AX9 HMC3 H35 H 0 0 N N N N N N 16.623 9.785 38.331 -2.272 5.126 1.162 HMC3 AX9 77 AX9 HMD2 H36 H 0 0 N N N N N N 20.388 6.477 34.538 5.147 2.447 1.574 HMD2 AX9 78 AX9 HMD3 H37 H 0 0 N N N N N N 18.814 5.791 35.065 5.208 4.092 0.897 HMD3 AX9 79 AX9 HMD1 H38 H 0 0 N N N N N N 18.951 6.601 33.468 3.875 3.624 1.979 HMD1 AX9 80 AX9 HNA H39 H 0 1 N N N N N N 10.056 7.182 29.934 1.279 -1.342 1.704 HNA AX9 81 AX9 H3 H41 H 0 1 N N N N N N 11.363 10.594 42.441 -7.588 3.807 -0.656 H3 AX9 82 AX9 H4 H42 H 0 1 N N N N N N 10.638 12.166 33.905 -7.552 -4.009 0.258 H4 AX9 83 # 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 AX9 CMA C2A SING N N 1 AX9 OA C1A DOUB N N 2 AX9 C2A C1A SING N N 3 AX9 C2A C3A DOUB N N 4 AX9 C1A NA SING N N 5 AX9 CBA CAA SING N N 6 AX9 C3A CAA SING N N 7 AX9 C3A C4A SING N N 8 AX9 NA C4A SING N N 9 AX9 C4A CHA DOUB N Z 10 AX9 CHA C1B SING N N 11 AX9 CMB C2B SING N N 12 AX9 O1B CGB DOUB N N 13 AX9 C1B C2B DOUB Y N 14 AX9 C1B NB SING Y N 15 AX9 C2B C3B SING Y N 16 AX9 CGB CBB SING N N 17 AX9 CGB O2B SING N N 18 AX9 NB C4B SING Y N 19 AX9 CBB CAB SING N N 20 AX9 C3B C4B DOUB Y N 21 AX9 C3B CAB SING N N 22 AX9 C4B CHB SING N N 23 AX9 CMD C2D SING N N 24 AX9 CBD CAD SING N N 25 AX9 C2D C1D SING N N 26 AX9 C2D C3D DOUB N N 27 AX9 C1D ND SING N N 28 AX9 C1D CHC SING N N 29 AX9 NC C1C SING N N 30 AX9 NC C4C DOUB N N 31 AX9 CHB C1C DOUB N Z 32 AX9 C3D CAD SING N N 33 AX9 C3D C4D SING N N 34 AX9 ND C4D SING N N 35 AX9 CHC C4C SING N N 36 AX9 C1C C2C SING N N 37 AX9 C4D OD DOUB N N 38 AX9 C4C C3C SING N N 39 AX9 C2C C3C DOUB N N 40 AX9 C2C CAC SING N N 41 AX9 C3C CMC SING N N 42 AX9 CAC CBC SING N N 43 AX9 CBC CGC SING N N 44 AX9 O2C CGC DOUB N N 45 AX9 CGC O1C SING N N 46 AX9 NB HNB SING N N 47 AX9 ND HND SING N N 48 AX9 C1D H1D1 SING N N 49 AX9 CAA HAA1 SING N N 50 AX9 CAA HAA2 SING N N 51 AX9 CAB HAB2 SING N N 52 AX9 CAB HAB1 SING N N 53 AX9 CAC HAC1 SING N N 54 AX9 CAC HAC2 SING N N 55 AX9 CAD HAD2 SING N N 56 AX9 CAD HAD1 SING N N 57 AX9 CBA HBA3 SING N N 58 AX9 CBA HBA2 SING N N 59 AX9 CBA HBA1 SING N N 60 AX9 CBB HBB2 SING N N 61 AX9 CBB HBB1 SING N N 62 AX9 CBC HBC1 SING N N 63 AX9 CBC HBC2 SING N N 64 AX9 CBD HBD3 SING N N 65 AX9 CBD HBD2 SING N N 66 AX9 CBD HBD1 SING N N 67 AX9 CHA HHA1 SING N N 68 AX9 CHB HHB1 SING N N 69 AX9 CHC HHC2 SING N N 70 AX9 CHC HHC1 SING N N 71 AX9 CMA HMA2 SING N N 72 AX9 CMA HMA1 SING N N 73 AX9 CMA HMA3 SING N N 74 AX9 CMB HMB1 SING N N 75 AX9 CMB HMB3 SING N N 76 AX9 CMB HMB2 SING N N 77 AX9 CMC HMC2 SING N N 78 AX9 CMC HMC1 SING N N 79 AX9 CMC HMC3 SING N N 80 AX9 CMD HMD2 SING N N 81 AX9 CMD HMD3 SING N N 82 AX9 CMD HMD1 SING N N 83 AX9 NA HNA SING N N 84 AX9 O1C H3 SING N N 85 AX9 O2B H4 SING N N 86 # 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 AX9 SMILES ACDLabs 12.01 "O=C(O)CCc1c(C)c(/C=C2\NC(=O)C(C)=C2CC)[NH]c1/C=C1\N=C(CC2NC(=O)C(CC)=C2C)C(C)=C1CCC(=O)O" AX9 InChI InChI 1.03 "InChI=1S/C33H40N4O6/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/h14-15,26,35H,7-13H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b27-14-,28-15-/t26-/m1/s1" AX9 InChIKey InChI 1.03 MZFCOERRVCGRTL-ZTYGKHTCSA-N AX9 SMILES_CANONICAL CACTVS 3.385 "CCC1=C(C)[C@@H](CC2=NC(=C/c3[nH]c(/C=C/4NC(=O)C(=C/4CC)C)c(C)c3CCC(O)=O)\C(=C2C)CCC(O)=O)NC1=O" AX9 SMILES CACTVS 3.385 "CCC1=C(C)[CH](CC2=NC(=Cc3[nH]c(C=C4NC(=O)C(=C4CC)C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O)NC1=O" AX9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC1=C([C@H](NC1=O)CC2=N/C(=C\c3c(c(c([nH]3)/C=C\4/C(=C(C(=O)N4)C)CC)C)CCC(=O)O)/C(=C2C)CCC(=O)O)C" AX9 SMILES "OpenEye OEToolkits" 2.0.7 "CCC1=C(C(NC1=O)CC2=NC(=Cc3c(c(c([nH]3)C=C4C(=C(C(=O)N4)C)CC)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 AX9 "SYSTEMATIC NAME" ACDLabs 12.01 "3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{[(2R)-4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid" AX9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[2-[(~{Z})-[5-[[(2~{R})-4-ethyl-3-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-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 AX9 "Create component" 2021-11-11 RCSB AX9 "Modify synonyms" 2021-12-01 RCSB AX9 "Modify synonyms" 2022-09-15 RCSB AX9 "Initial release" 2023-02-15 RCSB AX9 "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 AX9 "15,16-DIHYDROBILIVERDIN (double Cys bound form)" PDB ? 2 AX9 "3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{[(2R)-4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid" PDB ? # 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 AX9 CYS None Crosslinker "Amino-acid side chain" "Any position" CAD SG ? ? 2 AX9 CYS None Crosslinker "Amino-acid side chain" "Any position" CBA SG ? ? #