data_BYY # _chem_comp.id BYY _chem_comp.name "5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N2 O3 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms selenobiotin _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-04-18 _chem_comp.pdbx_modified_date 2020-06-17 _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 291.206 _chem_comp.one_letter_code ? _chem_comp.three_letter_code BYY _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 5JD2 _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 BYY O3 O1 O 0 1 N N N 19.601 2.621 4.225 2.868 -2.872 -1.168 O3 BYY 1 BYY C3 C1 C 0 1 N N N 19.776 1.419 4.024 2.800 -1.933 -0.398 C3 BYY 2 BYY N1 N1 N 0 1 N N N 19.123 0.470 4.703 3.700 -0.940 -0.376 N1 BYY 3 BYY N2 N2 N 0 1 N N N 20.610 0.936 3.096 1.816 -1.794 0.501 N2 BYY 4 BYY C4 C2 C 0 1 N N S 20.652 -0.564 3.171 2.039 -0.555 1.264 C4 BYY 5 BYY C5 C3 C 0 1 N N R 19.555 -0.887 4.238 3.319 0.026 0.668 C5 BYY 6 BYY C6 C4 C 0 1 N N N 18.364 -1.593 3.576 3.179 1.426 0.030 C6 BYY 7 BYY SE1 SE1 SE 0 0 N N N 18.450 -0.853 1.772 1.245 1.457 -0.438 SE1 BYY 8 BYY C2 C5 C 0 1 N N S 20.330 -1.253 1.825 0.787 0.343 1.141 C2 BYY 9 BYY C7 C6 C 0 1 N N N 21.066 -0.579 0.654 -0.464 -0.497 0.876 C7 BYY 10 BYY C8 C7 C 0 1 N N N 20.634 -1.218 -0.667 -1.652 0.429 0.605 C8 BYY 11 BYY C9 C8 C 0 1 N N N 21.548 -0.800 -1.829 -2.903 -0.410 0.340 C9 BYY 12 BYY C10 C9 C 0 1 N N N 21.286 -1.672 -3.062 -4.090 0.516 0.069 C10 BYY 13 BYY C11 C10 C 0 1 N N N 22.141 -2.949 -3.054 -5.323 -0.311 -0.192 C11 BYY 14 BYY O11 O2 O 0 1 N N N 23.245 -2.900 -2.467 -6.493 0.292 -0.456 O11 BYY 15 BYY O12 O3 O 0 1 N N N 21.674 -3.939 -3.656 -5.258 -1.518 -0.165 O12 BYY 16 BYY H1 H1 H 0 1 N N N 18.445 0.641 5.418 4.476 -0.869 -0.953 H1 BYY 17 BYY H2 H2 H 0 1 N N N 21.129 1.492 2.447 1.079 -2.410 0.629 H2 BYY 18 BYY H3 H3 H 0 1 N N N 21.633 -0.902 3.537 2.200 -0.798 2.314 H3 BYY 19 BYY H4 H4 H 0 1 N N N 19.971 -1.489 5.059 4.095 0.060 1.433 H4 BYY 20 BYY H5 H5 H 0 1 N N N 17.416 -1.338 4.073 3.419 2.209 0.749 H5 BYY 21 BYY H6 H6 H 0 1 N N N 18.493 -2.685 3.571 3.799 1.513 -0.862 H6 BYY 22 BYY H7 H7 H 0 1 N N N 20.456 -2.345 1.852 0.661 0.959 2.031 H7 BYY 23 BYY H8 H8 H 0 1 N N N 22.151 -0.706 0.783 -0.296 -1.135 0.008 H8 BYY 24 BYY H9 H9 H 0 1 N N N 20.822 0.493 0.638 -0.678 -1.116 1.747 H9 BYY 25 BYY H10 H10 H 0 1 N N N 19.604 -0.905 -0.894 -1.820 1.067 1.472 H10 BYY 26 BYY H11 H11 H 0 1 N N N 20.670 -2.312 -0.562 -1.438 1.049 -0.266 H11 BYY 27 BYY H12 H12 H 0 1 N N N 22.598 -0.914 -1.522 -2.735 -1.049 -0.528 H12 BYY 28 BYY H13 H13 H 0 1 N N N 21.352 0.252 -2.082 -3.116 -1.030 1.211 H13 BYY 29 BYY H14 H14 H 0 1 N N N 21.523 -1.091 -3.965 -4.258 1.154 0.936 H14 BYY 30 BYY H15 H15 H 0 1 N N N 20.223 -1.956 -3.077 -3.877 1.135 -0.802 H15 BYY 31 BYY H16 H16 H 0 1 N N N 23.684 -3.739 -2.547 -7.255 -0.280 -0.617 H16 BYY 32 # # 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 BYY O12 C11 DOUB N N 1 BYY C10 C11 SING N N 2 BYY C10 C9 SING N N 3 BYY C11 O11 SING N N 4 BYY C9 C8 SING N N 5 BYY C8 C7 SING N N 6 BYY C7 C2 SING N N 7 BYY SE1 C2 SING N N 8 BYY SE1 C6 SING N N 9 BYY C2 C4 SING N N 10 BYY N2 C4 SING N N 11 BYY N2 C3 SING N N 12 BYY C4 C5 SING N N 13 BYY C6 C5 SING N N 14 BYY C3 O3 DOUB N N 15 BYY C3 N1 SING N N 16 BYY C5 N1 SING N N 17 BYY N1 H1 SING N N 18 BYY N2 H2 SING N N 19 BYY C4 H3 SING N N 20 BYY C5 H4 SING N N 21 BYY C6 H5 SING N N 22 BYY C6 H6 SING N N 23 BYY C2 H7 SING N N 24 BYY C7 H8 SING N N 25 BYY C7 H9 SING N N 26 BYY C8 H10 SING N N 27 BYY C8 H11 SING N N 28 BYY C9 H12 SING N N 29 BYY C9 H13 SING N N 30 BYY C10 H14 SING N N 31 BYY C10 H15 SING N N 32 BYY O11 H16 SING N N 33 # # 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 BYY SMILES ACDLabs 12.01 "O=C1NC2C(N1)C([Se]C2)CCCCC(O)=O" BYY InChI InChI 1.03 "InChI=1S/C10H16N2O3Se/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1" BYY InChIKey InChI 1.03 HVUDXAKXEONARI-ZKWXMUAHSA-N BYY SMILES_CANONICAL CACTVS 3.385 "OC(=O)CCCC[C@@H]1[Se]C[C@@H]2NC(=O)N[C@H]12" BYY SMILES CACTVS 3.385 "OC(=O)CCCC[CH]1[Se]C[CH]2NC(=O)N[CH]12" BYY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1[C@H]2[C@@H]([C@@H]([Se]1)CCCCC(=O)O)NC(=O)N2" BYY SMILES "OpenEye OEToolkits" 2.0.4 "C1C2C(C([Se]1)CCCCC(=O)O)NC(=O)N2" # # 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 BYY "SYSTEMATIC NAME" ACDLabs 12.01 "5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid" BYY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydroselenopheno[3,4-d]imidazol-4-yl]pentanoic 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 BYY "Create component" 2016-04-18 RCSB BYY "Initial release" 2016-11-16 RCSB BYY "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id BYY _pdbx_chem_comp_synonyms.name selenobiotin _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##