data_J1R # _chem_comp.id J1R _chem_comp.name "(1R,19R) cobalt tetradehydrocorrin" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H37 Co N4 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2014-06-19 _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 612.604 _chem_comp.one_letter_code ? _chem_comp.three_letter_code J1R _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 3WFU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_comp_type "metal-containing ligand" _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 J1R O1B O1B O 0 1 N N N N N N 10.334 8.673 15.349 7.079 2.181 -0.676 O1B J1R 1 J1R CGB CGB C 0 1 N N N N N N 10.751 8.770 14.182 6.324 3.262 -0.810 CGB J1R 2 J1R O2B O2B O 0 1 N N N N N N 10.103 9.281 13.180 6.805 4.380 -0.821 O2B J1R 3 J1R CBB CBB C 0 1 N N N N N N 12.151 8.154 14.077 4.845 3.014 -0.946 CBB J1R 4 J1R CAB CAB C 0 1 N N N N N N 12.086 7.052 13.009 4.136 2.773 0.385 CAB J1R 5 J1R C3B C3B C 0 1 Y N N N N N 11.907 5.680 13.629 2.662 2.488 0.260 C3B J1R 6 J1R C2B C2B C 0 1 Y N N N N N 12.879 4.777 13.996 1.650 3.409 0.259 C2B J1R 7 J1R CMB CMB C 0 1 N N N N N N 14.365 4.930 13.892 1.825 4.901 0.375 CMB J1R 8 J1R C1B C1B C 0 1 Y N N N N N 12.211 3.661 14.502 0.470 2.722 0.115 C1B J1R 9 J1R NB NB N -1 1 Y N N N N N 10.861 3.853 14.511 0.737 1.394 0.045 NB J1R 10 J1R C4B C4B C 0 1 Y N N N N N 10.725 5.052 13.925 2.080 1.242 0.130 C4B J1R 11 J1R CHB CHB C 0 1 N N N N N N 9.374 5.592 13.685 2.687 -0.026 0.076 CHB J1R 12 J1R CHA CHA C 0 1 N N N N N N 12.909 2.443 14.985 -0.874 3.190 0.066 CHA J1R 13 J1R C4A C4A C 0 1 N N N N N N 12.221 1.310 15.542 -2.053 2.449 -0.158 C4A J1R 14 J1R NA NA N 0 1 N N N N N N 10.910 1.449 15.577 -2.034 1.162 -0.424 NA J1R 15 J1R CO CO CO ? 0 N N N N N N 9.574 2.584 15.082 -0.584 0.010 -0.053 CO J1R 16 J1R C3A C3A C 0 1 N N N N N N 12.723 0.136 16.096 -3.440 2.950 -0.097 C3A J1R 17 J1R C6A C6A C 0 1 N N N N N N 14.182 -0.219 16.148 -3.861 4.357 0.237 C6A J1R 18 J1R C2A C2A C 0 1 N N N N N N 11.588 -0.570 16.523 -4.241 1.895 -0.385 C2A J1R 19 J1R C5A C5A C 0 1 N N N N N N 11.673 -1.922 17.221 -5.746 1.905 -0.448 C5A J1R 20 J1R C1A C1A C 0 1 N N R N N N 10.348 0.289 16.394 -3.400 0.657 -0.658 C1A J1R 21 J1R CAA CAA C 0 1 N N N N N N 10.037 0.703 17.863 -3.414 0.317 -2.149 CAA J1R 22 J1R C4D C4D C 0 1 N N R N N N 9.018 -0.045 15.775 -3.452 -0.574 0.333 C4D J1R 23 J1R ND ND N 0 1 N N N N N N 8.334 1.279 15.606 -2.083 -1.110 0.203 ND J1R 24 J1R CAD CAD C 0 1 N N N N N N 9.383 -0.727 14.433 -3.570 -0.233 1.820 CAD J1R 25 J1R C3D C3D C 0 1 N N N N N N 7.892 -0.880 16.296 -4.296 -1.794 -0.003 C3D J1R 26 J1R C6D C6D C 0 1 N N N N N N 7.972 -2.339 16.690 -5.801 -1.772 -0.054 C6D J1R 27 J1R C2D C2D C 0 1 N N N N N N 6.676 -0.210 16.167 -3.499 -2.864 -0.239 C2D J1R 28 J1R C5D C5D C 0 1 N N N N N N 5.282 -0.704 16.386 -3.926 -4.258 -0.617 C5D J1R 29 J1R C1D C1D C 0 1 N N N N N N 7.034 1.090 15.719 -2.110 -2.396 -0.066 C1D J1R 30 J1R CHC CHC C 0 1 N N N N N N 6.235 2.279 15.424 -0.934 -3.163 -0.198 CHC J1R 31 J1R C4C C4C C 0 1 N N N N N N 6.798 3.520 14.803 0.420 -2.725 -0.141 C4C J1R 32 J1R C3C C3C C 0 1 N N N N N N 6.012 4.559 14.346 1.592 -3.438 -0.192 C3C J1R 33 J1R CMC CMC C 0 1 N N N N N N 4.497 4.690 14.337 1.743 -4.933 -0.296 CMC J1R 34 J1R NC NC N 0 1 N N N N N N 8.141 3.726 14.594 0.710 -1.403 -0.048 NC J1R 35 J1R C1C C1C C 0 1 N N N N N N 8.140 4.941 14.034 2.058 -1.280 -0.026 C1C J1R 36 J1R C2C C2C C 0 1 N N N N N N 6.907 5.477 13.826 2.621 -2.539 -0.112 C2C J1R 37 J1R CAC CAC C 0 1 N N N N N N 6.588 6.810 13.186 4.094 -2.857 -0.121 CAC J1R 38 J1R CBD CBD C 0 1 N N N N N N 6.523 6.577 11.663 4.689 -3.114 1.262 CBD J1R 39 J1R CGD CGD C 0 1 N N N N N N 6.177 7.778 10.801 6.176 -3.359 1.246 CGD J1R 40 J1R O2C O2C O 0 1 N N N N N N 4.983 8.184 10.796 6.937 -2.275 1.188 O2C J1R 41 J1R O1C O1C O 0 1 N N N N N N 7.095 8.275 10.103 6.656 -4.477 1.284 O1C J1R 42 J1R H1 H1 H 0 1 N N N N N N 9.457 9.033 15.403 6.668 1.403 -0.675 H1 J1R 43 J1R H2 H2 H 0 1 N N N N N N 12.446 7.723 15.045 4.439 3.797 -1.385 H2 J1R 44 J1R H3 H3 H 0 1 N N N N N N 12.879 8.923 13.781 4.699 2.237 -1.533 H3 J1R 45 J1R H4 H4 H 0 1 N N N N N N 13.021 7.062 12.429 4.574 2.019 0.837 H4 J1R 46 J1R H5 H5 H 0 1 N N N N N N 11.237 7.254 12.339 4.275 3.556 0.962 H5 J1R 47 J1R H6 H6 H 0 1 N N N N N N 14.855 4.022 14.273 0.988 5.352 0.186 H6 J1R 48 J1R H7 H7 H 0 1 N N N N N N 14.645 5.083 12.839 2.494 5.203 -0.261 H7 J1R 49 J1R H8 H8 H 0 1 N N N N N N 14.687 5.798 14.487 2.114 5.124 1.275 H8 J1R 50 J1R H9 H9 H 0 1 N N N N N N 9.305 6.558 13.207 3.633 -0.037 0.114 H9 J1R 51 J1R H10 H10 H 0 1 N N N N N N 13.986 2.406 14.915 -0.984 4.120 0.205 H10 J1R 52 J1R H11 H11 H 0 1 N N N N N N 14.305 -1.197 16.636 -4.590 4.629 -0.340 H11 J1R 53 J1R H12 H12 H 0 1 N N N N N N 14.584 -0.266 15.125 -3.121 4.966 0.108 H12 J1R 54 J1R H13 H13 H 0 1 N N N N N N 14.725 0.547 16.721 -4.151 4.398 1.161 H13 J1R 55 J1R H14 H14 H 0 1 N N N N N N 10.659 -2.277 17.459 -6.064 1.112 -0.896 H14 J1R 56 J1R H15 H15 H 0 1 N N N N N N 12.169 -2.646 16.558 -6.048 2.681 -0.940 H15 J1R 57 J1R H16 H16 H 0 1 N N N N N N 12.253 -1.819 18.150 -6.107 1.934 0.448 H16 J1R 58 J1R H17 H17 H 0 1 N N N N N N 9.636 -0.162 18.411 -4.267 -0.036 -2.390 H17 J1R 59 J1R H18 H18 H 0 1 N N N N N N 10.961 1.049 18.350 -2.741 -0.332 -2.339 H18 J1R 60 J1R H19 H19 H 0 1 N N N N N N 9.295 1.515 17.866 -3.242 1.104 -2.660 H19 J1R 61 J1R H20 H20 H 0 1 N N N N N N 9.879 -1.688 14.633 -4.431 0.139 1.995 H20 J1R 62 J1R H21 H21 H 0 1 N N N N N N 8.467 -0.901 13.849 -2.900 0.401 2.060 H21 J1R 63 J1R H22 H22 H 0 1 N N N N N N 10.062 -0.075 13.864 -3.456 -1.024 2.341 H22 J1R 64 J1R H23 H23 H 0 1 N N N N N N 6.985 -2.681 17.036 -6.095 -1.790 -0.975 H23 J1R 65 J1R H24 H24 H 0 1 N N N N N N 8.283 -2.937 15.821 -6.135 -0.972 0.370 H24 J1R 66 J1R H25 H25 H 0 1 N N N N N N 8.706 -2.460 17.500 -6.157 -2.541 0.412 H25 J1R 67 J1R H26 H26 H 0 1 N N N N N N 5.312 -1.747 16.733 -4.685 -4.527 -0.079 H26 J1R 68 J1R H27 H27 H 0 1 N N N N N N 4.787 -0.080 17.144 -3.203 -4.882 -0.466 H27 J1R 69 J1R H28 H28 H 0 1 N N N N N N 4.721 -0.648 15.442 -4.175 -4.278 -1.554 H28 J1R 70 J1R H29 H29 H 0 1 N N N N N N 5.183 2.261 15.667 -1.053 -4.091 -0.345 H29 J1R 71 J1R H30 H30 H 0 1 N N N N N N 4.049 3.809 14.820 0.884 -5.366 -0.174 H30 J1R 72 J1R H31 H31 H 0 1 N N N N N N 4.204 5.597 14.886 2.353 -5.249 0.390 H31 J1R 73 J1R H32 H32 H 0 1 N N N N N N 4.141 4.759 13.298 2.096 -5.163 -1.170 H32 J1R 74 J1R H33 H33 H 0 1 N N N N N N 7.376 7.540 13.423 4.261 -3.642 -0.686 H33 J1R 75 J1R H34 H34 H 0 1 N N N N N N 5.620 7.183 13.552 4.582 -2.112 -0.536 H34 J1R 76 J1R H35 H35 H 0 1 N N N N N N 5.763 5.804 11.477 4.494 -2.343 1.844 H35 J1R 77 J1R H36 H36 H 0 1 N N N N N N 7.508 6.208 11.340 4.250 -3.902 1.656 H36 J1R 78 J1R H37 H37 H 0 1 N N N N N N 4.898 8.911 10.190 6.527 -1.498 1.162 H37 J1R 79 # 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 J1R O1C CGD DOUB N N 1 N N J1R O2C CGD SING N N 2 N N J1R CGD CBD SING N N 3 N N J1R CBD CAC SING N N 4 N N J1R CAB C3B SING N N 5 N N J1R CAB CBB SING N N 6 N N J1R O2B CGB DOUB N N 7 N N J1R CAC C2C SING N N 8 N N J1R C3B C4B SING Y N 9 N N J1R C3B C2B DOUB Y N 10 N N J1R CHB C4B DOUB N N 11 N N J1R CHB C1C SING N N 12 N N J1R C2C C1C SING N N 13 N N J1R C2C C3C DOUB N N 14 N N J1R CMB C2B SING N N 15 N N J1R C4B NB SING Y N 16 N N J1R C2B C1B SING Y N 17 N N J1R C1C NC DOUB N N 18 N N J1R CBB CGB SING N N 19 N N J1R CGB O1B SING N N 20 N N J1R CMC C3C SING N N 21 N N J1R C3C C4C SING N N 22 N N J1R CAD C4D SING N N 23 N N J1R C1B NB SING Y N 24 N N J1R C1B CHA DOUB N N 25 N N J1R NB CO SING N N 26 Y N J1R NC C4C SING N N 27 N N J1R NC CO SING N N 28 Y N J1R C4C CHC DOUB N N 29 N N J1R CHA C4A SING N N 30 N N J1R CO NA SING N N 31 Y N J1R CO ND SING N N 32 Y N J1R CHC C1D SING N N 33 N N J1R C4A NA DOUB N N 34 N N J1R C4A C3A SING N N 35 N N J1R NA C1A SING N N 36 N N J1R ND C1D DOUB N N 37 N N J1R ND C4D SING N N 38 N N J1R C1D C2D SING N N 39 N N J1R C4D C3D SING N N 40 N N J1R C4D C1A SING N N 41 N N J1R C3A C6A SING N N 42 N N J1R C3A C2A DOUB N N 43 N N J1R C2D C3D DOUB N N 44 N N J1R C2D C5D SING N N 45 N N J1R C3D C6D SING N N 46 N N J1R C1A C2A SING N N 47 N N J1R C1A CAA SING N N 48 N N J1R C2A C5A SING N N 49 N N J1R O1B H1 SING N N 50 N N J1R CBB H2 SING N N 51 N N J1R CBB H3 SING N N 52 N N J1R CAB H4 SING N N 53 N N J1R CAB H5 SING N N 54 N N J1R CMB H6 SING N N 55 N N J1R CMB H7 SING N N 56 N N J1R CMB H8 SING N N 57 N N J1R CHB H9 SING N N 58 N N J1R CHA H10 SING N N 59 N N J1R C6A H11 SING N N 60 N N J1R C6A H12 SING N N 61 N N J1R C6A H13 SING N N 62 N N J1R C5A H14 SING N N 63 N N J1R C5A H15 SING N N 64 N N J1R C5A H16 SING N N 65 N N J1R CAA H17 SING N N 66 N N J1R CAA H18 SING N N 67 N N J1R CAA H19 SING N N 68 N N J1R CAD H20 SING N N 69 N N J1R CAD H21 SING N N 70 N N J1R CAD H22 SING N N 71 N N J1R C6D H23 SING N N 72 N N J1R C6D H24 SING N N 73 N N J1R C6D H25 SING N N 74 N N J1R C5D H26 SING N N 75 N N J1R C5D H27 SING N N 76 N N J1R C5D H28 SING N N 77 N N J1R CHC H29 SING N N 78 N N J1R CMC H30 SING N N 79 N N J1R CMC H31 SING N N 80 N N J1R CMC H32 SING N N 81 N N J1R CAC H33 SING N N 82 N N J1R CAC H34 SING N N 83 N N J1R CBD H35 SING N N 84 N N J1R CBD H36 SING N N 85 N N J1R O2C H37 SING N N 86 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 J1R InChI InChI 1.03 "InChI=1S/C33H38N4O4.Co/c1-16-20(5)32(7)33(8)21(6)17(2)27(37-33)14-25-19(4)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)18(3)24(34-28)13-26(16)36-32;/h13-15H,9-12H2,1-8H3,(H3,34,35,36,37,38,39,40,41);/q;+2/p-1/t32-,33-;/m1./s1" J1R InChIKey InChI 1.03 DBXMOQHUTDEXAY-ZNBLAKOKSA-M J1R SMILES_CANONICAL CACTVS 3.385 "CC1=C(C)[C@@]2(C)N|3=C1C=C4N|5=C(C=c6n7[Co+]|3|5|N8=C(C=c7c(C)c6CCC(O)=O)C(=C(C)[C@]28C)C)C(=C4C)CCC(O)=O" J1R SMILES CACTVS 3.385 "CC1=C(C)[C]2(C)N|3=C1C=C4N|5=C(C=c6n7[Co+]|3|5|N8=C(C=c7c(C)c6CCC(O)=O)C(=C(C)[C]28C)C)C(=C4C)CCC(O)=O" J1R SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=C([C@@]2([C@]3(C(=C(C4=[N]3[Co+]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C)C)C)C" J1R SMILES "OpenEye OEToolkits" 1.7.6 "CC1=C(C2(C3(C(=C(C4=[N]3[Co+]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C)C)C)C" # 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 J1R CO 6 octahedral octahedral OCT MetalCoord 2 J1R CO 4 square-planar "square planar" SPL MetalCoord 3 J1R CO 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 J1R CO "@OCT{Co,N,N,N,N,N,O}" MetalCoord 2 1 J1R CO "@OCT{Co,C,N,N,N,N,N}" MetalCoord 3 2 J1R CO "@SPL{Co,N,N,N,N}" MetalCoord 4 3 J1R CO "@SQP{Co,N,N,N,N,N}" MetalCoord # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id J1R _pdbx_chem_comp_pcm.modified_residue_id HIS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Metal coordination" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom CO _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? _pdbx_chem_comp_pcm.position "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 J1R "Create component" 2014-06-19 PDBJ J1R "Modify name" 2014-11-10 PDBJ J1R "Initial release" 2014-12-03 RCSB J1R "Other modification" 2026-07-17 RCSB J1R "Other modification" 2026-07-31 RCSB J1R "Other modification" 2026-09-16 RCSB #