data_HDD # _chem_comp.id HDD _chem_comp.name "CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C34 H32 Fe N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms HEME _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2000-08-22 _chem_comp.pdbx_modified_date 2026-09-16 _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 632.487 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1GGJ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y _chem_comp.pdbx_comp_type "metal-containing ligand" # 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 HDD FE FE FE ? 0 N N N N N N -1.372 4.997 -8.363 -0.609 0.241 0.197 FE HDD 1 HDD CHA CHA C 0 1 N N N N N N 1.937 5.951 -8.038 2.599 -0.545 -0.513 CHA HDD 2 HDD CHB CHB C 0 1 N N N N N N -1.768 7.424 -10.772 0.074 3.551 -0.217 CHB HDD 3 HDD CHC CHC C 0 1 N N N N N N -4.501 3.711 -8.970 -3.745 0.985 1.170 CHC HDD 4 HDD CHD CHD C 0 1 N N N N N N -0.984 2.863 -5.612 -1.523 -2.982 -0.443 CHD HDD 5 HDD NA "N A" N -1 1 Y N N N N N -0.087 6.296 -9.348 1.046 1.339 -0.300 NA HDD 6 HDD C1A C1A C 0 1 Y N N N N N 1.199 6.597 -8.974 2.298 0.851 -0.517 C1A HDD 7 HDD C2A C2A C 0 1 Y N N N N N 1.568 7.748 -9.842 3.172 1.886 -0.780 C2A HDD 8 HDD C3A C3A C 0 1 Y N N N N N 0.620 8.114 -10.701 2.457 3.043 -0.698 C3A HDD 9 HDD C4A C4A C 0 1 Y N N N N N -0.502 7.228 -10.312 1.156 2.696 -0.414 C4A HDD 10 HDD CMA CMA C 0 1 N N N N N N 0.554 9.266 -11.719 3.015 4.431 -0.890 CMA HDD 11 HDD CAA CAA C 0 1 N N N N N N 3.007 8.262 -9.885 4.644 1.750 -1.078 CAA HDD 12 HDD CBA CBA C 0 1 N N N N N N 3.216 9.566 -8.987 5.538 1.725 0.158 CBA HDD 13 HDD CGA CGA C 0 1 N N N N N N 4.682 9.963 -9.340 7.025 1.548 -0.139 CGA HDD 14 HDD O1A O1A O 0 1 N N N N N N 5.443 9.609 -8.422 7.462 0.385 -0.269 O1A HDD 15 HDD O2A O2A O -1 1 N N N N N N 4.810 10.242 -10.561 7.728 2.575 -0.238 O2A HDD 16 HDD NB "N B" N 0 1 N N N N N N -2.810 5.478 -9.643 -1.659 1.979 0.410 NB HDD 17 HDD C1B C1B C 0 1 N N N N N N -2.754 6.459 -10.551 -1.213 3.255 0.227 C1B HDD 18 HDD C2B C2B C 0 1 N N N N N N -4.055 6.550 -11.258 -2.196 4.171 0.597 C2B HDD 19 HDD C3B C3B C 0 1 N N N N N N -4.746 5.614 -10.585 -3.339 3.451 0.985 C3B HDD 20 HDD C4B C4B C 0 1 N N N N N N -3.970 4.733 -9.744 -2.959 2.112 0.897 C4B HDD 21 HDD CMB CMB C 0 1 N N N N N N -4.588 7.847 -11.935 -2.106 5.674 0.547 CMB HDD 22 HDD CAB CAB C 0 1 N N N N N N -6.242 5.252 -10.731 -4.601 4.088 1.462 CAB HDD 23 HDD CBB CBB C 0 1 N N N N N N -7.064 6.198 -10.906 -5.829 3.646 1.603 CBB HDD 24 HDD NC "N C" N -1 1 N N R N N N -2.416 3.341 -7.640 -2.364 -0.812 0.323 NC HDD 25 HDD C1C C1C C 0 1 N N N N N N -3.765 3.194 -7.940 -3.540 -0.350 0.829 C1C HDD 26 HDD C2C C2C C 0 1 N N N N N N -4.307 2.223 -6.986 -4.486 -1.372 0.876 C2C HDD 27 HDD C3C C3C C 0 1 N N N N N N -3.327 2.053 -6.068 -3.870 -2.560 0.439 C3C HDD 28 HDD C4C C4C C 0 1 N N N N N N -2.171 2.893 -6.376 -2.581 -2.168 0.076 C4C HDD 29 HDD CMC CMC C 0 1 N N N N N N -5.737 1.617 -6.933 -5.904 -1.274 1.376 CMC HDD 30 HDD CAC CAC C 0 1 N N N N N N -3.343 1.371 -4.698 -4.565 -3.879 0.350 CAC HDD 31 HDD CBC CBC C 0 1 N N N N N N -4.451 0.828 -4.392 -4.152 -5.113 0.180 CBC HDD 32 HDD ND "N D" N 0 1 N N N N N N 0.309 4.433 -7.215 0.371 -1.459 -0.373 ND HDD 33 HDD C1D C1D C 0 1 N N N N N N 0.033 3.611 -6.138 -0.190 -2.680 -0.630 C1D HDD 34 HDD C2D C2D C 0 1 N N S N N N 1.327 3.613 -5.289 0.837 -3.673 -1.194 C2D HDD 35 HDD C3D C3D C 0 1 N N R N N N 2.152 4.425 -5.806 2.119 -3.096 -0.508 C3D HDD 36 HDD C4D C4D C 0 1 N N N N N N 1.494 5.042 -7.021 1.729 -1.620 -0.479 C4D HDD 37 HDD CMD CMD C 0 1 N N N N N N 1.721 2.152 -4.934 0.736 -3.655 -2.719 CMD HDD 38 HDD CAD CAD C 0 1 N N N N N N 3.437 4.032 -6.622 3.462 -3.580 -1.037 CAD HDD 39 HDD CBD CBD C 0 1 N N N N N N 4.617 4.653 -5.894 4.369 -3.629 0.180 CBD HDD 40 HDD CGD CGD C 0 1 N N N N N N 4.079 5.739 -5.080 3.416 -3.754 1.326 CGD HDD 41 HDD O1D O1D O 0 1 N N N N N N 2.780 5.697 -5.156 2.152 -3.479 0.908 O1D HDD 42 HDD O2D O2D O 0 1 N N N N N N 4.619 6.672 -4.565 3.639 -4.058 2.468 O2D HDD 43 HDD OND OND O 0 1 N N N N N N 1.046 4.145 -3.894 0.667 -5.020 -0.738 OND HDD 44 HDD HHA HHA H 0 1 N N N N N N 2.999 6.147 -8.061 3.518 -0.758 -0.500 HHA HDD 45 HDD HHB HHB H 0 1 N N N N N N -2.011 8.329 -11.310 0.225 4.455 -0.448 HHB HDD 46 HDD HHC HHC H 0 1 N N N N N N -5.488 3.327 -9.180 -4.485 1.157 1.732 HHC HDD 47 HDD HHD HHD H 0 1 N N N N N N -0.888 2.300 -4.695 -1.795 -3.836 -0.733 HHD HDD 48 HDD HMA1 1HMA H 0 0 N N N N N N 0.868 8.901 -12.708 2.302 5.055 -1.097 HMA1 HDD 49 HDD HMA2 2HMA H 0 0 N N N N N N -0.477 9.644 -11.778 3.649 4.437 -1.624 HMA2 HDD 50 HDD HMA3 3HMA H 0 0 N N N N N N 1.224 10.077 -11.398 3.463 4.716 -0.076 HMA3 HDD 51 HDD HAA1 1HAA H 0 0 N N N N N N 3.676 7.470 -9.518 4.936 2.482 -1.662 HAA1 HDD 52 HDD HAA2 2HAA H 0 0 N N N N N N 3.264 8.506 -10.926 4.795 0.923 -1.587 HAA2 HDD 53 HDD HBA1 1HBA H 0 0 N N N N N N 2.508 10.361 -9.264 5.247 0.990 0.745 HBA1 HDD 54 HDD HBA2 2HBA H 0 0 N N N N N N 3.110 9.337 -7.916 5.416 2.567 0.655 HBA2 HDD 55 HDD H2A H2A H 0 1 N N N N N N 5.721 10.151 -10.813 -8.631 -0.845 0.543 H2A HDD 56 HDD HMB1 1HMB H 0 0 N N N N N N -5.571 7.648 -12.387 -2.963 6.049 0.287 HMB1 HDD 57 HDD HMB2 2HMB H 0 0 N N N N N N -4.686 8.641 -11.180 -1.440 5.950 -0.102 HMB2 HDD 58 HDD HMB3 3HMB H 0 0 N N N N N N -3.884 8.169 -12.716 -1.861 6.014 1.423 HMB3 HDD 59 HDD HAB HAB H 0 1 N N N N N N -6.575 4.225 -10.685 -4.518 4.982 1.755 HAB HDD 60 HDD HBB1 1HBB H 0 0 N N N N N N -8.117 5.985 -11.012 -6.490 4.210 1.969 HBB1 HDD 61 HDD HBB2 2HBB H 0 0 N N N N N N -6.712 7.218 -10.949 -6.060 2.782 1.308 HBB2 HDD 62 HDD HMC1 1HMC H 0 0 N N N N N N -5.808 0.917 -6.087 -6.493 -1.784 0.798 HMC1 HDD 63 HDD HMC2 2HMC H 0 0 N N N N N N -6.473 2.424 -6.804 -6.198 -0.350 1.377 HMC2 HDD 64 HDD HMC3 3HMC H 0 0 N N N N N N -5.943 1.080 -7.871 -5.954 -1.627 2.279 HMC3 HDD 65 HDD HAC HAC H 0 1 N N N N N N -2.483 1.353 -4.045 -5.507 -3.845 0.399 HAC HDD 66 HDD HBC1 1HBC H 0 0 N N N N N N -4.561 0.321 -3.444 -4.782 -5.811 0.106 HBC1 HDD 67 HDD HBC2 2HBC H 0 0 N N N N N N -5.283 0.873 -5.080 -3.231 -5.310 0.169 HBC2 HDD 68 HDD HMD1 1HMD H 0 0 N N N N N N 2.641 2.156 -4.331 1.353 -4.309 -3.096 HMD1 HDD 69 HDD HMD2 2HMD H 0 0 N N N N N N 0.908 1.682 -4.360 0.965 -2.766 -3.049 HMD2 HDD 70 HDD HMD3 3HMD H 0 0 N N N N N N 1.892 1.583 -5.860 -0.175 -3.876 -2.986 HMD3 HDD 71 HDD HAD1 1HAD H 0 0 N N N N N N 3.545 2.938 -6.657 3.814 -2.964 -1.707 HAD1 HDD 72 HDD HAD2 2HAD H 0 0 N N N N N N 3.372 4.427 -7.647 3.381 -4.467 -1.436 HAD2 HDD 73 HDD HBD1 1HBD H 0 0 N N N N N N 5.105 3.904 -5.253 4.903 -2.809 0.256 HBD1 HDD 74 HDD HBD2 2HBD H 0 0 N N N N N N 5.346 5.046 -6.618 4.973 -4.402 0.140 HBD2 HDD 75 HDD HND HND H 0 1 N N N N N N 1.848 4.140 -3.385 -0.051 -5.372 -0.979 HND HDD 76 # 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 _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag HDD FE NA SING N N 1 Y N HDD FE NB SING N N 2 Y N HDD FE NC SING N N 3 Y N HDD FE ND SING N N 4 Y N HDD CHA C1A SING N N 5 N N HDD CHA C4D DOUB N N 6 N N HDD CHA HHA SING N N 7 N N HDD CHB C4A SING N N 8 N N HDD CHB C1B DOUB N N 9 N N HDD CHB HHB SING N N 10 N N HDD CHC C4B SING N N 11 N N HDD CHC C1C DOUB N N 12 N N HDD CHC HHC SING N N 13 N N HDD CHD C4C DOUB N N 14 N N HDD CHD C1D SING N N 15 N N HDD CHD HHD SING N N 16 N N HDD NA C1A SING Y N 17 N N HDD NA C4A SING Y N 18 N N HDD C1A C2A DOUB Y N 19 N N HDD C2A C3A SING Y N 20 N N HDD C2A CAA SING N N 21 N N HDD C3A C4A DOUB Y N 22 N N HDD C3A CMA SING N N 23 N N HDD CMA HMA1 SING N N 24 N N HDD CMA HMA2 SING N N 25 N N HDD CMA HMA3 SING N N 26 N N HDD CAA CBA SING N N 27 N N HDD CAA HAA1 SING N N 28 N N HDD CAA HAA2 SING N N 29 N N HDD CBA CGA SING N N 30 N N HDD CBA HBA1 SING N N 31 N N HDD CBA HBA2 SING N N 32 N N HDD CGA O1A DOUB N N 33 N N HDD CGA O2A SING N N 34 N N HDD O2A H2A SING N N 35 N N HDD NB C1B SING N N 36 N N HDD NB C4B DOUB N N 37 N N HDD C1B C2B SING N N 38 N N HDD C2B C3B DOUB N N 39 N N HDD C2B CMB SING N N 40 N N HDD C3B C4B SING N N 41 N N HDD C3B CAB SING N N 42 N N HDD CMB HMB1 SING N N 43 N N HDD CMB HMB2 SING N N 44 N N HDD CMB HMB3 SING N N 45 N N HDD CAB CBB DOUB N N 46 N N HDD CAB HAB SING N N 47 N N HDD CBB HBB1 SING N N 48 N N HDD CBB HBB2 SING N N 49 N N HDD NC C1C SING N N 50 N N HDD NC C4C SING N N 51 N N HDD C1C C2C SING N N 52 N N HDD C2C C3C DOUB N N 53 N N HDD C2C CMC SING N N 54 N N HDD C3C C4C SING N N 55 N N HDD C3C CAC SING N N 56 N N HDD CMC HMC1 SING N N 57 N N HDD CMC HMC2 SING N N 58 N N HDD CMC HMC3 SING N N 59 N N HDD CAC CBC DOUB N N 60 N N HDD CAC HAC SING N N 61 N N HDD CBC HBC1 SING N N 62 N N HDD CBC HBC2 SING N N 63 N N HDD ND C1D DOUB N N 64 N N HDD ND C4D SING N N 65 N N HDD C1D C2D SING N N 66 N N HDD C2D C3D SING N N 67 N N HDD C2D CMD SING N N 68 N N HDD C2D OND SING N N 69 N N HDD C3D C4D SING N N 70 N N HDD C3D CAD SING N N 71 N N HDD C3D O1D SING N N 72 N N HDD CMD HMD1 SING N N 73 N N HDD CMD HMD2 SING N N 74 N N HDD CMD HMD3 SING N N 75 N N HDD CAD CBD SING N N 76 N N HDD CAD HAD1 SING N N 77 N N HDD CAD HAD2 SING N N 78 N N HDD CBD CGD SING N N 79 N N HDD CBD HBD1 SING N N 80 N N HDD CBD HBD2 SING N N 81 N N HDD CGD O1D SING N N 82 N N HDD CGD O2D DOUB N N 83 N N HDD OND HND SING N N 84 N N # 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 HDD SMILES ACDLabs 14.52 "O=C(O)CCc1c(C)c2C=C3C(C)=C(C=C)C=4C=C5N6C(=CC7=N8C(=Cc1n2[Fe]68N3=4)C1(CCC(=O)O1)C7(C)O)C(C=C)=C5C" HDD InChI InChI 1.06 "InChI=1S/C34H33N4O5.Fe/c1-7-20-17(3)23-13-24-19(5)22(9-10-31(39)40)28(37-24)16-30-34(12-11-32(41)43-34)33(6,42)29(38-30)15-27-21(8-2)18(4)25(36-27)14-26(20)35-23;/h7-8,13-16,42H,1-2,9-12H2,3-6H3,(H2-,35,36,37,38,39,40);/q-1;+2/p-1/t33-,34+;/m0./s1" HDD InChIKey InChI 1.06 HMYRFFHHXXPRDI-XCVPDAMTSA-M HDD SMILES_CANONICAL CACTVS 3.385 "Cc1c(CCC(O)=O)c2C=C3N=C(C=C4[N@@]5[Fe]n2c1C=C6N=C(C=C5C(=C4C=C)C)C(=C6C)C=C)[C@](C)(O)[C@@]37CCC(=O)O7" HDD SMILES CACTVS 3.385 "Cc1c(CCC(O)=O)c2C=C3N=C(C=C4[N]5[Fe]n2c1C=C6N=C(C=C5C(=C4C=C)C)C(=C6C)C=C)[C](C)(O)[C]37CCC(=O)O7" HDD SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C6=[N]4[Fe]37[N]8=C(C=C9N7C(=C6)C(=C9C)C=C)C(=C(C8=C2)C)C=C)(C)O" HDD SMILES "OpenEye OEToolkits" 3.1.0.0 "Cc1c2n3c(c1CCC(=O)O)C=C4C5(CCC(=O)O5)C(C6=[N]4[Fe]37[N]8=C(C=C9N7C(=C6)C(=C9C)C=C)C(=C(C8=C2)C)C=C)(C)O" # 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 HDD "SYSTEMATIC NAME" ACDLabs 14.52 "(T-4-S)-[(2R,5'S,21'S,23'R)-20'-(2-carboxyethyl)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxospiro[oxolane-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.1~3,6~.1~8,11~.1~13,16~]tetracosa[1(20),2,6(24),7,9,11,13(22),14,16,18]decaene[21,23]diide]-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]iron" HDD "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 ;3-[(19~{S},20~{R})-10,15-bis(ethenyl)-5,9,14,19-tetramethyl-19-oxidanyl-5'-oxidanylidene-spiro[2,22$l^{4},23,25$l^{4}-tetraza-1$l^{4}-ferraoctacyclo[11.9.1.1^{1,8}.1^{3,21}.0^{2,6}.0^{16,23}.0^{18,22}.0^{11,25}]pentacosa-3,5,7,9,11(25),12,14,16,18(22),21(24)-decaene-20,2'-oxolane]-4-yl]propanoic acid ; # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id HDD _pdbx_chem_comp_synonyms.name HEME _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_atom_coordination.geometry_id _pdbx_chem_comp_atom_coordination.comp_id _pdbx_chem_comp_atom_coordination.atom_id _pdbx_chem_comp_atom_coordination.number _pdbx_chem_comp_atom_coordination.geometry_calculated _pdbx_chem_comp_atom_coordination.geometry_generic _pdbx_chem_comp_atom_coordination.geometry_abbr _pdbx_chem_comp_atom_coordination.provenance 1 HDD FE 6 octahedron octahedral OCT FindGeo 1 HDD FE 6 octahedral octahedral OCT MetalCoord 2 HDD FE 5 "square pyramid" "square pyramidal" SPY FindGeo 2 HDD FE 5 square-pyramid "square pyramidal" SQP MetalCoord # loop_ _pdbx_chem_comp_atom_coordination_sphere.id _pdbx_chem_comp_atom_coordination_sphere.geometry_id _pdbx_chem_comp_atom_coordination_sphere.comp_id _pdbx_chem_comp_atom_coordination_sphere.atom_id _pdbx_chem_comp_atom_coordination_sphere.descriptor _pdbx_chem_comp_atom_coordination_sphere.provenance 1 1 HDD FE "@OCT{Fe,N,N,N,N,O,O}" MetalCoord 2 1 HDD FE "@OCT{Fe,N,N,N,N,N,O}" MetalCoord 3 2 HDD FE "@SQP{Fe,N,N,N,N,O}" MetalCoord 4 2 HDD FE "@SQP{Fe,N,N,N,N,N}" MetalCoord # 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.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 _pdbx_chem_comp_pcm.position 1 HDD GLU None "Metal coordination" "Any position" FE OE2 ? ? "Amino-acid side chain" 2 HDD HIS None "Metal coordination" "Any position" FE NE2 ? ? "Amino-acid side chain" 3 HDD TYR None "Metal coordination" "Any position" FE OH ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site HDD "Create component" 2000-08-22 RCSB HDD "Modify descriptor" 2011-06-04 RCSB HDD "Modify synonyms" 2020-06-05 PDBE HDD "Other modification" 2026-07-08 RCSB HDD "Other modification" 2026-07-17 RCSB HDD "Other modification" 2026-07-31 RCSB HDD "Other modification" 2026-09-16 RCSB #