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                    2023-02-10 
_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 
# 
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 
AX9 NB   N1  N 0 1 Y 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 17.646 9.695  35.902 2.011  1.941  -1.362 ND   AX9 2  
AX9 OD   O1  O 0 1 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 10.757 6.211  28.200 3.316  -1.497 2.037  C1A  AX9 4  
AX9 C1B  C2  C 0 1 Y 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 13.137 8.449  36.199 -1.638 1.193  0.424  C1C  AX9 6  
AX9 C1D  C4  C 0 1 N N R 17.504 8.422  35.277 2.356  2.223  0.038  C1D  AX9 7  
AX9 C2A  C5  C 0 1 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 9.959  7.227  32.805 -1.103 -3.223 -0.883 C2B  AX9 9  
AX9 C2C  C7  C 0 1 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 18.931 7.938  35.154 3.746  2.817  0.008  C2D  AX9 11 
AX9 C3A  C9  C 0 1 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 10.019 7.967  33.943 -2.138 -2.317 -0.738 C3B  AX9 13 
AX9 C3C  C11 C 0 1 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 19.773 8.783  35.755 4.124  2.857  -1.266 C3D  AX9 15 
AX9 C4A  C13 C 0 1 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 11.310 7.907  34.438 -1.608 -1.159 -0.165 C4B  AX9 17 
AX9 C4C  C15 C 0 1 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 18.986 9.902  36.209 3.060  2.318  -2.118 C4D  AX9 19 
AX9 CAA  C17 C 0 1 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 8.865  8.715  34.579 -3.577 -2.540 -1.127 CAB  AX9 21 
AX9 CAC  C19 C 0 1 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 21.274 8.634  35.905 5.449  3.379  -1.760 CAD  AX9 23 
AX9 CBA  C21 C 0 1 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 8.388  9.859  33.685 -4.339 -3.140 0.057  CBB  AX9 25 
AX9 CBC  C23 C 0 1 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 21.896 9.519  34.848 6.429  2.215  -1.919 CBD  AX9 27 
AX9 CGB  C25 C 0 1 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 11.826 10.033 40.766 -5.840 3.301  0.120  CGC  AX9 29 
AX9 CHA  C27 C 0 1 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 11.852 8.536  35.698 -2.323 0.003  0.155  CHB  AX9 31 
AX9 CHC  C29 C 0 1 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 12.096 4.555  26.755 5.771  -2.312 1.737  CMA  AX9 33 
AX9 CMB  C31 C 0 1 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 15.800 9.154  38.697 -1.299 4.729  1.451  CMC  AX9 35 
AX9 CMD  C33 C 0 1 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 10.676 6.510  29.529 2.125  -1.748 1.460  NA   AX9 37 
AX9 NC   N4  N 0 1 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 9.871  10.995 32.171 -6.155 -3.071 -1.443 O1B  AX9 39 
AX9 O1C  O3  O 0 1 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 9.982  11.592 34.282 -6.640 -3.885 0.554  O2B  AX9 41 
AX9 O2C  O5  O 0 1 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 10.084 6.768  27.326 3.510  -0.723 2.957  OA   AX9 43 
AX9 HNB  H1  H 0 1 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 16.902 10.336 36.089 1.183  1.551  -1.682 HND  AX9 45 
AX9 H1D1 H3  H 0 0 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 13.140 3.687  30.807 3.878  -3.960 -1.474 HAA1 AX9 47 
AX9 HAA2 H5  H 0 0 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 9.193  9.127  35.545 -4.030 -1.588 -1.405 HAB2 AX9 49 
AX9 HAB1 H7  H 0 0 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 13.234 10.768 38.591 -4.131 1.761  1.556  HAC1 AX9 51 
AX9 HAC2 H9  H 0 0 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 21.570 7.586  35.747 5.310  3.871  -2.722 HAD2 AX9 53 
AX9 HAD1 H11 H 0 0 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 14.323 2.041  29.463 4.726  -6.118 -0.595 HBA3 AX9 55 
AX9 HBA2 H13 H 0 0 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 13.704 2.799  27.956 3.190  -5.670 0.184  HBA1 AX9 57 
AX9 HBB2 H15 H 0 0 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 8.019  9.432  32.741 -4.293 -2.455 0.903  HBB1 AX9 59 
AX9 HBC1 H17 H 0 0 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 13.594 8.921  40.213 -4.285 2.229  -0.874 HBC2 AX9 61 
AX9 HBD3 H19 H 0 0 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 21.564 9.190  33.852 6.568  1.723  -0.956 HBD2 AX9 63 
AX9 HBD1 H21 H 0 0 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 12.567 5.099  31.892 1.561  -4.066 -0.988 HHA1 AX9 65 
AX9 HHB1 H23 H 0 0 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 16.639 6.541  35.628 1.662  3.466  1.654  HHC2 AX9 67 
AX9 HHC1 H26 H 0 0 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 12.862 3.784  26.927 5.967  -1.622 2.557  HMA2 AX9 69 
AX9 HMA1 H28 H 0 0 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 12.497 5.326  26.081 6.349  -2.011 0.863  HMA3 AX9 71 
AX9 HMB1 H30 H 0 0 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 8.056  7.893  32.057 -2.010 -4.636 -2.200 HMB3 AX9 73 
AX9 HMB2 H32 H 0 0 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 15.203 9.718  39.428 -1.193 4.778  2.534  HMC2 AX9 75 
AX9 HMC1 H34 H 0 0 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 16.623 9.785  38.331 -2.272 5.126  1.162  HMC3 AX9 77 
AX9 HMD2 H36 H 0 0 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 18.814 5.791  35.065 5.208  4.092  0.897  HMD3 AX9 79 
AX9 HMD1 H38 H 0 0 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 10.056 7.182  29.934 1.279  -1.342 1.704  HNA  AX9 81 
AX9 H3   H41 H 0 1 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 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 
# 
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 ? 
# 
