data_HDE # _chem_comp.id HDE _chem_comp.name "CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C34 H38 Fe N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-10-20 _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 638.534 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HDE _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 3P9P _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 HDE FE FE FE 0 0 N N S N N N -1.381 4.930 -8.679 0.936 -0.064 0.143 FE HDE 1 HDE NA NA N 0 1 N N R N N N 0.100 4.353 -7.424 -0.349 -1.369 0.519 NA HDE 2 HDE NB NB N 0 1 Y N N N N N -2.527 3.477 -7.902 2.009 -1.190 -0.891 NB HDE 3 HDE NC NC N 0 1 Y N N N N N -2.833 5.473 -9.976 2.342 0.975 0.780 NC HDE 4 HDE ND ND N 0 1 Y N N N N N -0.155 6.408 -9.495 -0.287 1.344 0.025 ND HDE 5 HDE C1A C1A C 0 1 N N N N N N 1.356 5.059 -7.284 -1.666 -1.120 0.872 C1A HDE 6 HDE O1A O1A O 0 1 N N N N N N 2.470 5.827 -5.188 -3.602 -2.641 0.956 O1A HDE 7 HDE C1B C1B C 0 1 Y N N N N N -2.358 2.964 -6.601 1.655 -2.449 -1.319 C1B HDE 8 HDE C1C C1C C 0 1 Y N N N N N -4.199 5.077 -9.899 3.673 0.675 0.728 C1C HDE 9 HDE C1D C1D C 0 1 Y N N N N N -0.421 7.375 -10.396 -0.020 2.680 0.084 C1D HDE 10 HDE O1D O1D O 0 1 N N N N N N 5.367 9.849 -8.212 -6.046 3.049 -1.673 O1D HDE 11 HDE C2A C2A C 0 1 N N R N N N 2.128 4.679 -6.004 -2.255 -2.381 1.437 C2A HDE 12 HDE O2A O2A O 0 1 N N N N N N 4.420 6.822 -4.380 -5.486 -1.505 1.524 O2A HDE 13 HDE C2B C2B C 0 1 Y N N N N N -3.540 2.377 -6.091 2.555 -2.799 -2.273 C2B HDE 14 HDE C2C C2C C 0 1 Y N N N N N -5.131 5.893 -10.549 4.292 1.479 1.604 C2C HDE 15 HDE C2D C2D C 0 1 Y N N N N N 0.619 8.253 -10.710 -1.131 3.333 -0.299 C2D HDE 16 HDE O2D O2D O 0 1 N N N N N N 4.946 10.665 -10.197 -5.671 2.585 -3.801 O2D HDE 17 HDE C3A C3A C 0 1 N N S N N N 1.213 3.769 -5.202 -1.288 -3.478 0.993 C3A HDE 18 HDE C3B C3B C 0 1 Y N N N N N -4.582 2.642 -7.106 3.624 -1.880 -2.184 C3B HDE 19 HDE C3C C3C C 0 1 Y N N N N N -4.291 7.012 -11.044 3.378 2.514 1.917 C3C HDE 20 HDE C3D C3D C 0 1 Y N N N N N 1.726 7.787 -9.917 -2.185 2.396 -0.308 C3D HDE 21 HDE C4A C4A C 0 1 N N N N N N -0.015 3.679 -6.142 -0.230 -2.721 0.236 C4A HDE 22 HDE C4B C4B C 0 1 Y N N N N N -3.907 3.363 -8.072 3.332 -1.031 -1.184 C4B HDE 23 HDE C4C C4C C 0 1 Y N N N N N -2.890 6.714 -10.635 2.270 2.272 1.205 C4C HDE 24 HDE C4D C4D C 0 1 Y N N N N N 1.147 6.630 -9.209 -1.656 1.203 0.072 C4D HDE 25 HDE CAA CAA C 0 1 N N N N N N 3.470 3.965 -6.290 -2.351 -2.339 2.964 CAA HDE 26 HDE CAB CAB C 0 1 N N N N N N -6.060 2.311 -7.096 4.859 -1.855 -3.047 CAB HDE 27 HDE CAC CAC C 0 1 N N N N N N -4.561 8.304 -11.812 3.607 3.663 2.865 CAC HDE 28 HDE CAD CAD C 0 1 N N N N N N 3.136 8.292 -9.855 -3.624 2.666 -0.668 CAD HDE 29 HDE CBA CBA C 0 1 N N N N N N 4.608 4.842 -5.758 -3.845 -2.104 3.196 CBA HDE 30 HDE CBB CBB C 0 1 N N N N N N -6.574 1.894 -5.755 4.606 -0.976 -4.274 CBB HDE 31 HDE CBC CBC C 0 1 N N N N N N -5.959 8.787 -11.870 4.209 4.844 2.100 CBC HDE 32 HDE CBD CBD C 0 1 N N N N N N 3.145 9.578 -9.015 -3.823 2.446 -2.169 CBD HDE 33 HDE CGA CGA C 0 1 N N N N N N 3.883 5.943 -5.037 -4.436 -2.028 1.814 CGA HDE 34 HDE CGD CGD C 0 1 N N N N N N 4.571 10.092 -9.148 -5.261 2.715 -2.529 CGD HDE 35 HDE CHA CHA C 0 1 N N N N N N 1.920 5.846 -8.229 -2.327 0.029 0.643 CHA HDE 36 HDE CHB CHB C 0 1 N N N N N N -1.074 2.872 -5.894 0.634 -3.260 -0.645 CHB HDE 37 HDE CHC CHC C 0 1 N N N N N N -4.557 3.786 -9.292 4.283 -0.218 -0.331 CHC HDE 38 HDE CHD CHD C 0 1 N N N N N N -1.750 7.559 -10.981 1.246 3.256 0.682 CHD HDE 39 HDE CMA CMA C 0 1 N N N N N N 1.750 2.334 -4.968 -0.681 -4.186 2.207 CMA HDE 40 HDE CMB CMB C 0 1 N N N N N N -3.699 1.660 -4.789 2.437 -3.948 -3.241 CMB HDE 41 HDE CMC CMC C 0 1 N N N N N N -6.616 5.645 -10.632 5.687 1.314 2.149 CMC HDE 42 HDE CMD CMD C 0 1 N N N N N N 0.580 9.402 -11.699 -1.231 4.795 -0.654 CMD HDE 43 HDE ONA ONA O 0 1 N N N N N N 1.038 4.384 -3.909 -1.946 -4.416 0.139 ONA HDE 44 HDE HAA HAA H 0 1 N N N N N N 3.487 2.987 -5.787 -2.035 -3.287 3.398 HAA HDE 45 HDE HAAA HAAA H 0 0 N N N N N N 3.589 3.815 -7.373 -1.762 -1.514 3.366 HAAA HDE 46 HDE HAB HAB H 0 1 N N N N N N -6.613 3.209 -7.409 5.694 -1.451 -2.476 HAB HDE 47 HDE HABA HABA H 0 0 N N N N N N -6.229 1.482 -7.799 5.096 -2.869 -3.370 HABA HDE 48 HDE HAC HAC H 0 1 N N N N N N -3.971 9.094 -11.325 2.658 3.964 3.308 HAC HDE 49 HDE HACA HACA H 0 0 N N N N N N -4.240 8.131 -12.850 4.294 3.353 3.653 HACA HDE 50 HDE HAD HAD H 0 1 N N N N N N 3.785 7.536 -9.390 -4.271 1.987 -0.112 HAD HDE 51 HDE HADA HADA H 0 0 N N N N N N 3.503 8.504 -10.870 -3.874 3.696 -0.415 HADA HDE 52 HDE HBA HBA H 0 1 N N N N N N 5.270 4.281 -5.081 -4.279 -2.935 3.752 HBA HDE 53 HDE HBAA HBAA H 0 0 N N N N N N 5.233 5.234 -6.574 -4.005 -1.167 3.731 HBAA HDE 54 HDE HBB HBB H 0 1 N N N N N N -7.649 1.671 -5.827 3.771 -1.381 -4.845 HBB HDE 55 HDE HBBA HBBA H 0 0 N N N N N N -6.035 0.996 -5.419 4.368 0.038 -3.951 HBBA HDE 56 HDE HBBB HBBB H 0 0 N N N N N N -6.416 2.708 -5.033 5.499 -0.958 -4.898 HBBB HDE 57 HDE HBC HBC H 0 1 N N N N N N -6.001 9.720 -12.451 4.375 5.675 2.785 HBC HDE 58 HDE HBCA HBCA H 0 0 N N N N N N -6.590 8.026 -12.352 5.158 4.543 1.657 HBCA HDE 59 HDE HBCB HBCB H 0 0 N N N N N N -6.325 8.974 -10.850 3.522 5.154 1.312 HBCB HDE 60 HDE HBD HBD H 0 1 N N N N N N 2.418 10.310 -9.396 -3.176 3.124 -2.725 HBD HDE 61 HDE HBDA HBDA H 0 0 N N N N N N 2.889 9.373 -7.965 -3.572 1.415 -2.421 HBDA HDE 62 HDE HHA HHA H 0 1 N N N N N N 2.998 5.903 -8.267 -3.378 0.089 0.886 HHA HDE 63 HDE HHB HHB H 0 1 N N N N N N -0.968 2.115 -5.131 0.574 -4.317 -0.861 HHB HDE 64 HDE HHC HHC H 0 1 N N N N N N -5.632 3.842 -9.064 4.876 0.410 -0.997 HHC HDE 65 HDE HHCA HHCA H 0 0 N N N N N N -4.325 3.018 -10.045 4.964 -0.910 0.165 HHCA HDE 66 HDE HHD HHD H 0 1 N N N N N N -2.051 8.579 -10.701 1.727 3.869 -0.081 HHD HDE 67 HDE HHDA HHDA H 0 0 N N N N N N -1.610 7.427 -12.064 0.960 3.912 1.504 HHDA HDE 68 HDE HMA HMA H 0 1 N N N N N N 1.018 1.759 -4.381 -1.460 -4.738 2.733 HMA HDE 69 HDE HMAA HMAA H 0 0 N N N N N N 1.911 1.840 -5.938 0.093 -4.878 1.874 HMAA HDE 70 HDE HMAB HMAB H 0 0 N N N N N N 2.702 2.384 -4.419 -0.243 -3.446 2.877 HMAB HDE 71 HDE HMB HMB H 0 1 N N N N N N -3.974 2.380 -4.004 1.935 -3.609 -4.148 HMB HDE 72 HDE HMBA HMBA H 0 0 N N N N N N -4.490 0.901 -4.883 3.432 -4.315 -3.493 HMBA HDE 73 HDE HMBB HMBB H 0 0 N N N N N N -2.751 1.171 -4.522 1.859 -4.751 -2.784 HMBB HDE 74 HDE HMC HMC H 0 1 N N N N N N -7.114 6.105 -9.766 6.394 1.835 1.503 HMC HDE 75 HDE HMCA HMCA H 0 0 N N N N N N -7.010 6.087 -11.559 5.737 1.732 3.154 HMCA HDE 76 HDE HMCB HMCB H 0 0 N N N N N N -6.807 4.562 -10.632 5.941 0.254 2.183 HMCB HDE 77 HDE HMD HMD H 0 1 N N N N N N 0.277 10.323 -11.180 -1.048 4.923 -1.720 HMD HDE 78 HDE HMDA HMDA H 0 0 N N N N N N 1.578 9.541 -12.139 -2.228 5.161 -0.409 HMDA HDE 79 HDE HMDB HMDB H 0 0 N N N N N N -0.144 9.175 -12.496 -0.489 5.358 -0.087 HMDB HDE 80 HDE HONA HONA H 0 0 N N N N N N 0.469 3.843 -3.375 -1.376 -5.133 -0.171 HONA HDE 81 HDE H38 H38 H 0 1 N N N N N N 5.874 10.858 -10.138 -6.602 2.769 -3.983 H38 HDE 82 # 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 HDE FE NA SING N N 1 HDE FE NB SING N N 2 HDE FE NC SING N N 3 HDE FE ND SING N N 4 HDE NA C1A SING N N 5 HDE NA C4A SING N N 6 HDE NB C1B SING Y N 7 HDE NB C4B SING Y N 8 HDE NC C1C SING Y N 9 HDE NC C4C SING Y N 10 HDE ND C1D SING Y N 11 HDE ND C4D SING Y N 12 HDE C1A C2A SING N N 13 HDE C1A CHA DOUB N N 14 HDE O1A C2A SING N N 15 HDE O1A CGA SING N N 16 HDE C1B C2B DOUB Y N 17 HDE C1B CHB SING N N 18 HDE C1C C2C DOUB Y N 19 HDE C1C CHC SING N N 20 HDE C1D C2D DOUB Y N 21 HDE C1D CHD SING N N 22 HDE O1D CGD DOUB N N 23 HDE C2A C3A SING N N 24 HDE C2A CAA SING N N 25 HDE O2A CGA DOUB N N 26 HDE C2B C3B SING Y N 27 HDE C2B CMB SING N N 28 HDE C2C C3C SING Y N 29 HDE C2C CMC SING N N 30 HDE C2D C3D SING Y N 31 HDE C2D CMD SING N N 32 HDE O2D CGD SING N N 33 HDE C3A C4A SING N N 34 HDE C3A CMA SING N N 35 HDE C3A ONA SING N N 36 HDE C3B C4B DOUB Y N 37 HDE C3B CAB SING N N 38 HDE C3C C4C DOUB Y N 39 HDE C3C CAC SING N N 40 HDE C3D C4D DOUB Y N 41 HDE C3D CAD SING N N 42 HDE C4A CHB DOUB N N 43 HDE C4B CHC SING N N 44 HDE C4C CHD SING N N 45 HDE C4D CHA SING N N 46 HDE CAA CBA SING N N 47 HDE CAA HAA SING N N 48 HDE CAA HAAA SING N N 49 HDE CAB CBB SING N N 50 HDE CAB HAB SING N N 51 HDE CAB HABA SING N N 52 HDE CAC CBC SING N N 53 HDE CAC HAC SING N N 54 HDE CAC HACA SING N N 55 HDE CAD CBD SING N N 56 HDE CAD HAD SING N N 57 HDE CAD HADA SING N N 58 HDE CBA CGA SING N N 59 HDE CBA HBA SING N N 60 HDE CBA HBAA SING N N 61 HDE CBB HBB SING N N 62 HDE CBB HBBA SING N N 63 HDE CBB HBBB SING N N 64 HDE CBC HBC SING N N 65 HDE CBC HBCA SING N N 66 HDE CBC HBCB SING N N 67 HDE CBD CGD SING N N 68 HDE CBD HBD SING N N 69 HDE CBD HBDA SING N N 70 HDE CHA HHA SING N N 71 HDE CHB HHB SING N N 72 HDE CHC HHC SING N N 73 HDE CHC HHCA SING N N 74 HDE CHD HHD SING N N 75 HDE CHD HHDA SING N N 76 HDE CMA HMA SING N N 77 HDE CMA HMAA SING N N 78 HDE CMA HMAB SING N N 79 HDE CMB HMB SING N N 80 HDE CMB HMBA SING N N 81 HDE CMB HMBB SING N N 82 HDE CMC HMC SING N N 83 HDE CMC HMCA SING N N 84 HDE CMC HMCB SING N N 85 HDE CMD HMD SING N N 86 HDE CMD HMDA SING N N 87 HDE CMD HMDB SING N N 88 HDE ONA HONA SING N N 89 HDE O2D H38 SING N N 90 # 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 HDE SMILES ACDLabs 12.01 "O=C(O)CCc9c(c4n6c9C=C8N5C(=Cc1c(c(c3n1[Fe]56n2c(c(c(c2C3)C)CC)C4)CC)C)C(O)(C)C87OC(=O)CC7)C" HDE SMILES_CANONICAL CACTVS 3.370 "CCc1c(C)c2Cc3n4c(C=C5[N@]6C(=Cc7n8c(Cc1n2[Fe@@]468)c(C)c7CCC(O)=O)[C@]9(CCC(=O)O9)[C@@]5(C)O)c(C)c3CC" HDE SMILES CACTVS 3.370 "CCc1c(C)c2Cc3n4c(C=C5[N]6C(=Cc7n8c(Cc1n2[Fe]468)c(C)c7CCC(O)=O)[C]9(CCC(=O)O9)[C]5(C)O)c(C)c3CC" HDE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CCc1c(c2n3c1Cc4c(c(c5n4[Fe]36n7c(c(c(c7C=C8N6C(=C5)[C@@]9([C@@]8(C)O)CCC(=O)O9)C)CC)C2)CCC(=O)O)C)C" HDE SMILES "OpenEye OEToolkits" 1.7.0 "CCc1c(c2n3c1Cc4c(c(c5n4[Fe]36n7c(c(c(c7C=C8N6C(=C5)C9(C8(C)O)CCC(=O)O9)C)CC)C2)CCC(=O)O)C)C" HDE InChI InChI 1.03 "InChI=1S/C34H38N4O5.Fe/c1-7-20-17(3)23-13-27-21(8-2)18(4)25(37-27)15-29-33(6,42)34(12-11-32(41)43-34)30(38-29)16-28-22(9-10-31(39)40)19(5)24(36-28)14-26(20)35-23;/h15-16,42H,7-14H2,1-6H3,(H,39,40);/q-4;+4/b29-15-,30-16-;/t33-,34+;/m0./s1" HDE InChIKey InChI 1.03 SQSYUADQFVTXKU-CAMYIWQSSA-N # _pdbx_chem_comp_identifier.comp_id HDE _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 12.01 _pdbx_chem_comp_identifier.identifier "{3-[(2R,5'S)-10',15'-diethyl-5'-hydroxy-5',9',14',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.1~3,6~.1~8,11~.1~13,16~]tetracosa[1(20),2,6,8,10,13,15,18]octaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato(4-)}iron" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site HDE "Create component" 2010-10-20 RCSB HDE "Modify aromatic_flag" 2011-06-04 RCSB HDE "Modify descriptor" 2011-06-04 RCSB HDE "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id HDE _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Heme/heme-like _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 CBC _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 ? #