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 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 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 _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 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 X2I "Modify PCM" 2024-09-27 PDBE # _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 ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id X2I _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 CAA _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 ? #