data_X2I
# 
_chem_comp.id                                    X2I 
_chem_comp.name                                  "(15,16)-DIHYDROBILIVERDIN (SINGLY LINKED)" 
_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                         "3-(2-{[3-(2-carboxyethyl)-5-{[(2R)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-1H-pyrrol-2-yl]methyl}-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-19 
_chem_comp.pdbx_modified_date                    2023-10-20 
_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                     X2I 
_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        7SUT 
_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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
X2I NA   N1  N 0 1 N N N N N N 9.777  -5.493  -59.303 -5.103 0.199  0.755  NA   X2I 1  
X2I C1A  C1  C 0 1 N N N N N N 9.707  -4.441  -58.460 -6.207 0.970  0.714  C1A  X2I 2  
X2I C2A  C2  C 0 1 N N N N N N 9.215  -3.355  -59.161 -7.119 0.400  -0.193 C2A  X2I 3  
X2I C3A  C3  C 0 1 N N N N N N 8.984  -3.744  -60.440 -6.556 -0.730 -0.704 C3A  X2I 4  
X2I C4A  C4  C 0 1 N N N N N N 9.340  -5.105  -60.528 -5.282 -0.868 -0.121 C4A  X2I 5  
X2I CMA  C5  C 0 1 N N N N N N 9.000  -1.974  -58.592 -8.481 0.945  -0.537 CMA  X2I 6  
X2I CBA  C6  C 0 1 N N N N N N 7.269  -3.395  -62.255 -6.710 -1.276 -3.118 CBA  X2I 7  
X2I OA   O1  O 0 1 N N N N N N 10.047 -4.510  -57.267 -6.385 1.992  1.355  OA   X2I 8  
X2I CHA  C7  C 0 1 N N N N N N 9.301  -5.883  -61.639 -4.378 -1.883 -0.366 CHA  X2I 9  
X2I CAA  C8  C 0 1 N N N N N N 8.466  -2.826  -61.521 -7.181 -1.659 -1.714 CAA  X2I 10 
X2I NB   N2  N 0 1 Y N N N N N 9.978  -7.846  -63.007 -2.458 -0.686 0.669  NB   X2I 11 
X2I C1B  C9  C 0 1 Y N N N N N 9.582  -7.354  -61.793 -3.077 -1.814 0.174  C1B  X2I 12 
X2I C2B  C10 C 0 1 Y N N N N N 9.457  -8.423  -60.938 -2.185 -2.868 0.304  C2B  X2I 13 
X2I C3B  C11 C 0 1 Y N N N N N 9.799  -9.557  -61.624 -1.024 -2.353 0.884  C3B  X2I 14 
X2I C4B  C12 C 0 1 Y N N N N N 10.097 -9.197  -62.921 -1.215 -1.027 1.097  C4B  X2I 15 
X2I CHB  C13 C 0 1 N N N N N N 10.512 -10.150 -64.036 -0.211 -0.085 1.708  CHB  X2I 16 
X2I CMB  C14 C 0 1 N N N N N N 9.030  -8.433  -59.496 -2.424 -4.299 -0.104 CMB  X2I 17 
X2I CAB  C15 C 0 1 N N N N N N 9.773  -10.970 -61.108 0.221  -3.133 1.217  CAB  X2I 18 
X2I CBB  C16 C 0 1 N N N N N N 10.794 -11.289 -60.024 1.172  -3.111 0.018  CBB  X2I 19 
X2I CGB  C17 C 0 1 N N N N N N 12.114 -11.736 -60.581 2.418  -3.891 0.351  CGB  X2I 20 
X2I O1B  O2  O 0 1 N N N N N N 12.272 -11.879 -61.818 2.534  -4.411 1.435  O1B  X2I 21 
X2I O2B  O3  O 0 1 N N N N N N 13.044 -11.973 -59.756 3.399  -4.007 -0.558 O2B  X2I 22 
X2I CHC  C18 C 0 1 N N N N N N 10.779 -7.679  -68.316 3.828  0.369  -1.330 CHC  X2I 23 
X2I NC   N3  N 0 1 Y N N N N N 10.571 -8.638  -65.991 1.942  -0.110 0.328  NC   X2I 24 
X2I C1C  C19 C 0 1 Y N N N N N 10.621 -9.874  -65.369 0.723  0.418  0.638  C1C  X2I 25 
X2I C2C  C20 C 0 1 Y N N N N N 10.858 -10.809 -66.358 0.498  1.466  -0.180 C2C  X2I 26 
X2I C3C  C21 C 0 1 Y N N N N N 10.945 -10.141 -67.571 1.618  1.591  -1.025 C3C  X2I 27 
X2I C4C  C22 C 0 1 Y N N N N N 10.772 -8.799  -67.330 2.488  0.617  -0.688 C4C  X2I 28 
X2I CMC  C23 C 0 1 N N N N N N 11.169 -10.757 -68.953 1.813  2.628  -2.101 CMC  X2I 29 
X2I CAC  C24 C 0 1 N N N N N N 10.967 -12.299 -66.161 -0.728 2.344  -0.188 CAC  X2I 30 
X2I CBC  C25 C 0 1 N N N N N N 12.404 -12.776 -66.171 -0.518 3.521  0.767  CBC  X2I 31 
X2I CGC  C26 C 0 1 N N N N N N 12.379 -14.303 -66.216 -1.743 4.398  0.759  CGC  X2I 32 
X2I O1C  O4  O 0 1 N N N N N N 12.578 -14.947 -65.149 -1.786 5.499  1.526  O1C  X2I 33 
X2I O2C  O5  O 0 1 N N N N N N 12.129 -14.920 -67.279 -2.687 4.112  0.061  O2C  X2I 34 
X2I ND   N4  N 0 1 N N N N N N 13.157 -7.811  -68.805 5.084  0.866  0.724  ND   X2I 35 
X2I C1D  C27 C 0 1 N N R N N N 12.087 -6.994  -68.305 4.882  1.264  -0.675 C1D  X2I 36 
X2I C2D  C28 C 0 1 N N N N N N 12.087 -5.861  -69.311 6.217  1.082  -1.359 C2D  X2I 37 
X2I C3D  C29 C 0 1 N N N N N N 12.991 -6.055  -70.263 7.073  0.628  -0.428 C3D  X2I 38 
X2I C4D  C30 C 0 1 N N N N N N 13.715 -7.275  -69.960 6.372  0.500  0.862  C4D  X2I 39 
X2I CMD  C31 C 0 1 N N N N N N 11.152 -4.691  -69.231 6.529  1.357  -2.807 CMD  X2I 40 
X2I CAD  C32 C 0 1 N N N N N N 13.084 -5.041  -71.391 8.498  0.314  -0.659 CAD  X2I 41 
X2I CBD  C33 C 0 1 N N N N N N 13.807 -5.247  -72.467 9.253  -0.120 0.341  CBD  X2I 42 
X2I OD   O6  O 0 1 N N N N N N 14.671 -7.868  -70.515 6.879  0.113  1.897  OD   X2I 43 
X2I HNA  H1  H 0 1 N N N N N N 10.099 -6.409  -59.064 -4.317 0.361  1.300  HNA  X2I 44 
X2I HMA2 H2  H 0 0 N N N N N N 9.276  -1.969  -57.527 -8.659 1.861  0.027  HMA2 X2I 45 
X2I HMA1 H3  H 0 0 N N N N N N 9.626  -1.252  -59.137 -8.526 1.162  -1.605 HMA1 X2I 46 
X2I HMA3 H4  H 0 0 N N N N N N 7.941  -1.695  -58.698 -9.242 0.208  -0.283 HMA3 X2I 47 
X2I HBA1 H5  H 0 0 N N N N N N 6.939  -2.684  -63.026 -7.009 -0.250 -3.334 HBA1 X2I 48 
X2I HBA2 H6  H 0 0 N N N N N N 7.549  -4.347  -62.730 -5.625 -1.357 -3.173 HBA2 X2I 49 
X2I HBA3 H7  H 0 0 N N N N N N 6.450  -3.568  -61.542 -7.162 -1.947 -3.848 HBA3 X2I 50 
X2I HHA1 H8  H 0 0 N N N N N N 9.027  -5.370  -62.549 -4.667 -2.730 -0.971 HHA1 X2I 51 
X2I HAA1 H9  H 0 0 N N N N N N 9.272  -2.650  -62.248 -6.882 -2.684 -1.497 HAA1 X2I 52 
X2I H1   H10 H 0 1 N N N N N N 8.173  -1.871  -61.060 -8.266 -1.577 -1.659 H1   X2I 53 
X2I HNB  H11 H 0 1 N N N N N N 10.152 -7.299  -63.826 -2.845 0.203  0.704  HNB  X2I 54 
X2I HHB1 H12 H 0 0 N N N N N N 9.792  -10.979 -63.979 -0.733 0.759  2.160  HHB1 X2I 55 
X2I H2   H13 H 0 1 N N N N N N 11.509 -10.510 -63.741 0.362  -0.610 2.473  H2   X2I 56 
X2I HMB1 H14 H 0 0 N N N N N N 7.938  -8.555  -59.437 -2.104 -4.440 -1.137 HMB1 X2I 57 
X2I HMB2 H15 H 0 0 N N N N N N 9.521  -9.268  -58.974 -1.854 -4.962 0.546  HMB2 X2I 58 
X2I HMB3 H16 H 0 0 N N N N N N 9.319  -7.483  -59.022 -3.485 -4.529 -0.018 HMB3 X2I 59 
X2I HAB1 H17 H 0 0 N N N N N N 8.771  -11.163 -60.697 0.713  -2.683 2.079  HAB1 X2I 60 
X2I HAB2 H18 H 0 0 N N N N N N 9.958  -11.645 -61.957 -0.046 -4.164 1.449  HAB2 X2I 61 
X2I HBB2 H19 H 0 0 N N N N N N 10.956 -10.386 -59.417 0.681  -3.561 -0.844 HBB2 X2I 62 
X2I HBB1 H20 H 0 0 N N N N N N 10.392 -12.091 -59.387 1.440  -2.080 -0.213 HBB1 X2I 63 
X2I H3   H21 H 0 1 N N N N N N 13.820 -12.257 -60.225 4.179  -4.517 -0.299 H3   X2I 64 
X2I HHC2 H22 H 0 0 N N N N N N 9.990  -6.959  -68.053 4.107  -0.677 -1.198 HHC2 X2I 65 
X2I HHC1 H23 H 0 0 N N N N N N 10.588 -8.080  -69.322 3.769  0.597  -2.395 HHC1 X2I 66 
X2I H4   H24 H 0 1 N N N N N N 10.412 -7.765  -65.531 2.354  -0.873 0.762  H4   X2I 67 
X2I HMC1 H25 H 0 0 N N N N N N 12.248 -10.802 -69.164 1.422  2.249  -3.046 HMC1 X2I 68 
X2I HMC3 H26 H 0 0 N N N N N N 10.748 -11.773 -68.974 1.281  3.539  -1.827 HMC3 X2I 69 
X2I HMC2 H27 H 0 0 N N N N N N 10.672 -10.139 -69.715 2.876  2.845  -2.208 HMC2 X2I 70 
X2I HAC2 H28 H 0 0 N N N N N N 10.514 -12.562 -65.194 -0.899 2.720  -1.196 HAC2 X2I 71 
X2I HAC1 H29 H 0 0 N N N N N N 10.421 -12.804 -66.971 -1.592 1.764  0.135  HAC1 X2I 72 
X2I HBC2 H30 H 0 0 N N N N N N 12.919 -12.435 -65.261 -0.347 3.145  1.775  HBC2 X2I 73 
X2I HBC1 H31 H 0 0 N N N N N N 12.925 -12.382 -67.056 0.346  4.101  0.444  HBC1 X2I 74 
X2I H5   H32 H 0 1 N N N N N N 12.503 -15.878 -65.322 -2.593 6.030  1.488  H5   X2I 75 
X2I HND  H33 H 0 1 N N N N N N 13.463 -8.661  -68.375 4.412  0.870  1.423  HND  X2I 76 
X2I H1D1 H34 H 0 0 N N N N N N 12.315 -6.608  -67.300 4.571  2.308  -0.727 H1D1 X2I 77 
X2I HMD2 H35 H 0 0 N N N N N N 10.515 -4.790  -68.340 6.857  2.391  -2.918 HMD2 X2I 78 
X2I HMD1 H36 H 0 0 N N N N N N 11.734 -3.760  -69.163 7.320  0.687  -3.142 HMD1 X2I 79 
X2I HMD3 H37 H 0 0 N N N N N N 10.521 -4.664  -70.132 5.635  1.194  -3.408 HMD3 X2I 80 
X2I HAD1 H38 H 0 0 N N N N N N 12.534 -4.115  -71.304 8.926  0.440  -1.643 HAD1 X2I 81 
X2I HBD2 H39 H 0 0 N N N N N N 13.844 -4.498  -73.244 8.825  -0.246 1.325  HBD2 X2I 82 
X2I HBD1 H40 H 0 0 N N N N N N 14.365 -6.165  -72.575 10.294 -0.350 0.172  HBD1 X2I 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 
X2I CBD CAD  DOUB N N 1  
X2I CAD C3D  SING N N 2  
X2I OD  C4D  DOUB N N 3  
X2I C3D C4D  SING N N 4  
X2I C3D C2D  DOUB N N 5  
X2I C4D ND   SING N N 6  
X2I C2D CMD  SING N N 7  
X2I C2D C1D  SING N N 8  
X2I CMC C3C  SING N N 9  
X2I ND  C1D  SING N N 10 
X2I CHC C1D  SING N N 11 
X2I CHC C4C  SING N N 12 
X2I C3C C4C  DOUB Y N 13 
X2I C3C C2C  SING Y N 14 
X2I C4C NC   SING Y N 15 
X2I O2C CGC  DOUB N N 16 
X2I C2C CAC  SING N N 17 
X2I C2C C1C  DOUB Y N 18 
X2I CGC CBC  SING N N 19 
X2I CGC O1C  SING N N 20 
X2I CBC CAC  SING N N 21 
X2I NC  C1C  SING Y N 22 
X2I C1C CHB  SING N N 23 
X2I CHB C4B  SING N N 24 
X2I NB  C4B  SING Y N 25 
X2I NB  C1B  SING Y N 26 
X2I C4B C3B  DOUB Y N 27 
X2I CBA CAA  SING N N 28 
X2I O1B CGB  DOUB N N 29 
X2I C1B CHA  SING N N 30 
X2I C1B C2B  DOUB Y N 31 
X2I CHA C4A  DOUB N Z 32 
X2I C3B CAB  SING N N 33 
X2I C3B C2B  SING Y N 34 
X2I CAA C3A  SING N N 35 
X2I CAB CBB  SING N N 36 
X2I C2B CMB  SING N N 37 
X2I CGB CBB  SING N N 38 
X2I CGB O2B  SING N N 39 
X2I C4A C3A  SING N N 40 
X2I C4A NA   SING N N 41 
X2I C3A C2A  DOUB N N 42 
X2I NA  C1A  SING N N 43 
X2I C2A CMA  SING N N 44 
X2I C2A C1A  SING N N 45 
X2I C1A OA   DOUB N N 46 
X2I NA  HNA  SING N N 47 
X2I CMA HMA2 SING N N 48 
X2I CMA HMA1 SING N N 49 
X2I CMA HMA3 SING N N 50 
X2I CBA HBA1 SING N N 51 
X2I CBA HBA2 SING N N 52 
X2I CBA HBA3 SING N N 53 
X2I CHA HHA1 SING N N 54 
X2I CAA HAA1 SING N N 55 
X2I CAA H1   SING N N 56 
X2I NB  HNB  SING N N 57 
X2I CHB HHB1 SING N N 58 
X2I CHB H2   SING N N 59 
X2I CMB HMB1 SING N N 60 
X2I CMB HMB2 SING N N 61 
X2I CMB HMB3 SING N N 62 
X2I CAB HAB1 SING N N 63 
X2I CAB HAB2 SING N N 64 
X2I CBB HBB2 SING N N 65 
X2I CBB HBB1 SING N N 66 
X2I O2B H3   SING N N 67 
X2I CHC HHC2 SING N N 68 
X2I CHC HHC1 SING N N 69 
X2I NC  H4   SING N N 70 
X2I CMC HMC1 SING N N 71 
X2I CMC HMC3 SING N N 72 
X2I CMC HMC2 SING N N 73 
X2I CAC HAC2 SING N N 74 
X2I CAC HAC1 SING N N 75 
X2I CBC HBC2 SING N N 76 
X2I CBC HBC1 SING N N 77 
X2I O1C H5   SING N N 78 
X2I ND  HND  SING N N 79 
X2I C1D H1D1 SING N N 80 
X2I CMD HMD2 SING N N 81 
X2I CMD HMD1 SING N N 82 
X2I CMD HMD3 SING N N 83 
X2I CAD HAD1 SING N N 84 
X2I CBD HBD2 SING N N 85 
X2I CBD HBD1 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 
X2I SMILES           ACDLabs              12.01 "O=C(O)CCc1c(C)c(/C=C2\NC(=O)C(C)=C2CC)[NH]c1Cc1[NH]c(CC2NC(=O)C(C=C)=C2C)c(C)c1CCC(=O)O"                                                                                                                                                                
X2I InChI            InChI                1.06  "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/h8,14,26,34-35H,2,7,9-13,15H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b27-14-/t26-/m1/s1" 
X2I InChIKey         InChI                1.06  VPVJAAZCMDJQMG-WLUDIELQSA-N                                                                                                                                                                                                                              
X2I SMILES_CANONICAL CACTVS               3.385 "CCC1=C(C)C(=O)N\C1=C/c2[nH]c(Cc3[nH]c(C[C@H]4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C"                                                                                                                                                            
X2I SMILES           CACTVS               3.385 "CCC1=C(C)C(=O)NC1=Cc2[nH]c(Cc3[nH]c(C[CH]4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C"                                                                                                                                                               
X2I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC\1=C(C(=O)N/C1=C\c2c(c(c([nH]2)Cc3c(c(c([nH]3)C[C@@H]4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)C"                                                                                                                                                    
X2I SMILES           "OpenEye OEToolkits" 2.0.7 "CCC1=C(C(=O)NC1=Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)CC4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)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 
X2I "SYSTEMATIC NAME" ACDLabs              12.01 "3-(2-{[3-(2-carboxyethyl)-5-{[(2R)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-1H-pyrrol-2-yl]methyl}-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid"                     
X2I "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[5-[[(2~{R})-4-ethenyl-3-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]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 
X2I "Create component" 2023-10-19 RCSB 
X2I "Initial release"  2023-10-25 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      X2I 
_pdbx_chem_comp_synonyms.name         "3-(2-{[3-(2-carboxyethyl)-5-{[(2R)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-1H-pyrrol-2-yl]methyl}-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
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