data_EEM # _chem_comp.id EEM _chem_comp.name "[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N6 O5 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Se-ADENOSYLSELENOMETHIONINE _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2008-09-03 _chem_comp.pdbx_modified_date 2021-03-01 _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 446.340 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EEM _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 3E5F _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.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 EEM C2 C2 C 0 1 Y N N 15.894 -7.528 -22.257 6.619 -0.225 1.323 C2 EEM 1 EEM N3 N3 N 0 1 Y N N 14.910 -8.366 -21.981 5.394 0.196 1.089 N3 EEM 2 EEM C4 C4 C 0 1 Y N N 14.208 -8.943 -22.968 4.584 -0.488 0.289 C4 EEM 3 EEM "C1'" "C1'" C 0 1 N N R 12.510 -10.391 -21.817 2.387 0.768 0.204 "C1'" EEM 4 EEM "C2'" "C2'" C 0 1 N N R 13.498 -10.983 -20.811 2.566 1.949 -0.775 "C2'" EEM 5 EEM "C3'" "C3'" C 0 1 N N S 12.648 -10.910 -19.545 1.135 2.498 -0.966 "C3'" EEM 6 EEM "C4'" "C4'" C 0 1 N N S 12.080 -9.500 -19.711 0.260 1.584 -0.079 "C4'" EEM 7 EEM "C5'" "C5'" C 0 1 N N N 13.216 -8.517 -19.425 -1.087 1.319 -0.754 "C5'" EEM 8 EEM O O O 0 1 N N N 16.917 -7.026 -16.200 -8.072 -1.236 0.629 O EEM 9 EEM C C C 0 1 N N N 16.214 -6.086 -16.631 -7.152 -1.728 0.020 C EEM 10 EEM OXT OXT O 0 1 N N N 15.317 -5.490 -15.995 -7.009 -3.062 -0.017 OXT EEM 11 EEM CA CA C 0 1 N N S 16.468 -5.633 -18.072 -6.165 -0.845 -0.698 CA EEM 12 EEM N N N 0 1 N N N 17.791 -6.095 -18.517 -6.765 0.478 -0.923 N EEM 13 EEM CB CB C 0 1 N N N 15.401 -6.238 -18.986 -4.902 -0.694 0.152 CB EEM 14 EEM CG CG C 0 1 N N N 13.998 -5.728 -18.647 -3.852 0.099 -0.630 CG EEM 15 EEM SE SE SE 1 0 N N S 12.697 -6.734 -19.513 -2.234 0.291 0.459 SE EEM 16 EEM CE CE C 0 1 N N N 11.349 -6.676 -18.254 -2.793 1.686 1.717 CE EEM 17 EEM "O4'" "O4'" O 0 1 N N N 11.740 -9.406 -21.105 1.013 0.357 0.040 "O4'" EEM 18 EEM "O3'" "O3'" O 0 1 N N N 11.588 -11.865 -19.614 1.055 3.855 -0.522 "O3'" EEM 19 EEM "O2'" "O2'" O 0 1 N N N 13.724 -12.356 -21.135 3.414 2.948 -0.204 "O2'" EEM 20 EEM N9 N9 N 0 1 Y N N 13.195 -9.803 -22.992 3.293 -0.329 -0.148 N9 EEM 21 EEM C8 C8 C 0 1 Y N N 12.887 -10.036 -24.268 3.008 -1.377 -0.972 C8 EEM 22 EEM N7 N7 N 0 1 Y N N 13.692 -9.335 -25.063 4.041 -2.163 -1.064 N7 EEM 23 EEM C5 C5 C 0 1 Y N N 14.522 -8.647 -24.287 5.051 -1.671 -0.308 C5 EEM 24 EEM N1 N1 N 0 1 Y N N 16.222 -7.224 -23.501 7.105 -1.328 0.782 N1 EEM 25 EEM C6 C6 C 0 1 Y N N 15.561 -7.758 -24.536 6.367 -2.079 -0.029 C6 EEM 26 EEM N6 N6 N 0 1 N N N 15.866 -7.420 -25.785 6.882 -3.236 -0.587 N6 EEM 27 EEM H2 H2 H 0 1 N N N 16.445 -7.079 -21.444 7.253 0.354 1.978 H2 EEM 28 EEM "H1'" "H1'" H 0 1 N N N 11.860 -11.179 -22.225 2.566 1.094 1.229 "H1'" EEM 29 EEM "H2'" "H2'" H 0 1 N N N 14.479 -10.489 -20.759 2.971 1.600 -1.724 "H2'" EEM 30 EEM "H3'" "H3'" H 0 1 N N N 13.180 -11.107 -18.603 0.832 2.421 -2.010 "H3'" EEM 31 EEM "H4'" "H4'" H 0 1 N N N 11.223 -9.291 -19.053 0.111 2.036 0.901 "H4'" EEM 32 EEM "H5'" "H5'" H 0 1 N N N 13.592 -8.714 -18.410 -1.568 2.268 -0.991 "H5'" EEM 33 EEM "H5'A" "H5'A" H 0 0 N N N 13.982 -8.671 -20.200 -0.929 0.753 -1.672 "H5'A" EEM 34 EEM HOXT HOXT H 0 0 N N N 15.246 -5.861 -15.123 -7.666 -3.588 0.459 HOXT EEM 35 EEM HA HA H 0 1 N N N 16.428 -4.535 -18.116 -5.906 -1.293 -1.658 HA EEM 36 EEM HN HN H 0 1 N N N 17.791 -6.200 -19.511 -7.564 0.413 -1.535 HN EEM 37 EEM HNA HNA H 0 1 N N N 18.484 -5.425 -18.253 -7.013 0.915 -0.048 HNA EEM 38 EEM HB HB H 0 1 N N N 15.633 -5.964 -20.026 -5.145 -0.165 1.073 HB EEM 39 EEM HBA HBA H 0 1 N N N 15.410 -7.329 -18.845 -4.506 -1.681 0.392 HBA EEM 40 EEM HG HG H 0 1 N N N 13.843 -5.802 -17.560 -3.609 -0.430 -1.552 HG EEM 41 EEM HGA HGA H 0 1 N N N 13.914 -4.683 -18.980 -4.248 1.086 -0.871 HGA EEM 42 EEM HE HE H 0 1 N N N 11.789 -6.664 -17.246 -3.324 2.471 1.177 HE EEM 43 EEM HEA HEA H 0 1 N N N 10.748 -5.767 -18.402 -3.453 1.254 2.469 HEA EEM 44 EEM HEB HEB H 0 1 N N N 10.707 -7.562 -18.364 -1.915 2.110 2.203 HEB EEM 45 EEM "HO3'" "HO3'" H 0 0 N N N 11.295 -12.077 -18.736 1.631 4.461 -1.007 "HO3'" EEM 46 EEM "HO2'" "HO2'" H 0 0 N N N 13.774 -12.455 -22.078 3.560 3.714 -0.777 "HO2'" EEM 47 EEM H8 H8 H 0 1 N N N 12.101 -10.695 -24.606 2.064 -1.532 -1.473 H8 EEM 48 EEM HN6 HN6 H 0 1 N N N 15.943 -6.425 -25.852 6.334 -3.775 -1.178 HN6 EEM 49 EEM HN6A HN6A H 0 0 N N N 16.737 -7.839 -26.040 7.792 -3.507 -0.386 HN6A EEM 50 # # 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 EEM N1 C2 DOUB Y N 1 EEM C2 N3 SING Y N 2 EEM C2 H2 SING N N 3 EEM C4 N3 DOUB Y N 4 EEM C5 C4 SING Y N 5 EEM N9 C4 SING Y N 6 EEM N9 "C1'" SING N N 7 EEM "C1'" "O4'" SING N N 8 EEM "C1'" "C2'" SING N N 9 EEM "C1'" "H1'" SING N N 10 EEM "O2'" "C2'" SING N N 11 EEM "C2'" "C3'" SING N N 12 EEM "C2'" "H2'" SING N N 13 EEM "C4'" "C3'" SING N N 14 EEM "O3'" "C3'" SING N N 15 EEM "C3'" "H3'" SING N N 16 EEM "O4'" "C4'" SING N N 17 EEM "C4'" "C5'" SING N N 18 EEM "C4'" "H4'" SING N N 19 EEM "C5'" "H5'" SING N N 20 EEM "C5'" "H5'A" SING N N 21 EEM "C5'" SE SING N N 22 EEM C O DOUB N N 23 EEM CA C SING N N 24 EEM C OXT SING N N 25 EEM OXT HOXT SING N N 26 EEM CB CA SING N N 27 EEM N CA SING N N 28 EEM CA HA SING N N 29 EEM N HN SING N N 30 EEM N HNA SING N N 31 EEM CB CG SING N N 32 EEM CB HB SING N N 33 EEM CB HBA SING N N 34 EEM SE CG SING N N 35 EEM CG HG SING N N 36 EEM CG HGA SING N N 37 EEM SE CE SING N N 38 EEM CE HE SING N N 39 EEM CE HEA SING N N 40 EEM CE HEB SING N N 41 EEM "O3'" "HO3'" SING N N 42 EEM "O2'" "HO2'" SING N N 43 EEM C8 N9 SING Y N 44 EEM N7 C8 DOUB Y N 45 EEM C8 H8 SING N N 46 EEM N7 C5 SING Y N 47 EEM C6 C5 DOUB Y N 48 EEM C6 N1 SING Y N 49 EEM N6 C6 SING N N 50 EEM N6 HN6 SING N N 51 EEM N6 HN6A SING N N 52 # # 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 EEM SMILES ACDLabs 10.04 "O=C(O)C(N)CC[Se+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O" EEM SMILES_CANONICAL CACTVS 3.341 "C[Se@@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" EEM SMILES CACTVS 3.341 "C[Se+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" EEM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[Se@@+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" EEM SMILES "OpenEye OEToolkits" 1.5.0 "C[Se+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" EEM InChI InChI 1.03 "InChI=1S/C15H22N6O5Se/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27-/m0/s1" EEM InChIKey InChI 1.03 GGJFWMOVUFBSIN-FCKMPRQPSA-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 EEM "SYSTEMATIC NAME" ACDLabs 10.04 "[(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylselenonium (non-preferred name)" EEM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EEM "Create component" 2008-09-03 RCSB EEM "Modify aromatic_flag" 2011-06-04 RCSB EEM "Modify descriptor" 2011-06-04 RCSB EEM "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EEM _pdbx_chem_comp_synonyms.name Se-ADENOSYLSELENOMETHIONINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##