data_D5V # _chem_comp.id D5V _chem_comp.name "(1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H15 N O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-20 _chem_comp.pdbx_modified_date 2020-04-17 _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 253.317 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D5V _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 5QB5 _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 D5V C4 C1 C 0 1 Y N N -4.718 1.116 11.171 3.202 1.154 0.075 C4 D5V 1 D5V C5 C2 C 0 1 Y N N -5.550 0.138 10.655 4.409 0.554 -0.222 C5 D5V 2 D5V C6 C3 C 0 1 N N R -1.586 3.013 10.219 -0.606 -0.272 0.770 C6 D5V 3 D5V C7 C4 C 0 1 N N S -0.054 2.997 10.258 -0.808 -0.820 -0.647 C7 D5V 4 D5V C8 C5 C 0 1 N N S 0.525 3.854 9.132 -1.576 0.210 -1.484 C8 D5V 5 D5V C9 C6 C 0 1 N N S -0.318 5.117 8.965 -2.845 0.615 -0.717 C9 D5V 6 D5V C10 C7 C 0 1 N N N -1.470 4.950 7.979 -3.499 -0.678 -0.174 C10 D5V 7 D5V C11 C8 C 0 1 N N R -2.118 4.472 10.095 -1.963 0.192 1.321 C11 D5V 8 D5V O2 O1 O 0 1 N N N 0.428 1.662 10.140 -1.555 -2.037 -0.585 O2 D5V 9 D5V N N1 N 0 1 N N N 1.939 4.226 9.454 -0.733 1.393 -1.703 N D5V 10 D5V O1 O2 O 0 1 N N N -1.023 5.356 10.204 -2.418 1.286 0.495 O1 D5V 11 D5V O O3 O 0 1 N N N -2.610 4.641 8.790 -2.914 -0.871 1.127 O D5V 12 D5V S S1 S 0 1 N N N -2.251 2.218 11.715 0.542 1.132 0.720 S D5V 13 D5V C3 C9 C 0 1 Y N N -3.342 0.990 11.044 2.083 0.371 0.334 C3 D5V 14 D5V C2 C10 C 0 1 Y N N -2.811 -0.113 10.392 2.184 -1.015 0.287 C2 D5V 15 D5V C1 C11 C 0 1 Y N N -3.654 -1.084 9.880 3.393 -1.608 -0.016 C1 D5V 16 D5V C C12 C 0 1 Y N N -5.020 -0.961 10.013 4.505 -0.825 -0.268 C D5V 17 D5V H1 H1 H 0 1 N N N -5.139 1.976 11.672 3.128 2.231 0.111 H1 D5V 18 D5V H2 H2 H 0 1 N N N -6.621 0.236 10.756 5.280 1.162 -0.419 H2 D5V 19 D5V H3 H3 H 0 1 N N N -1.943 2.420 9.364 -0.198 -1.055 1.409 H3 D5V 20 D5V H4 H4 H 0 1 N N N 0.270 3.424 11.218 0.162 -1.012 -1.105 H4 D5V 21 D5V H5 H5 H 0 1 N N N 0.501 3.279 8.194 -1.848 -0.228 -2.444 H5 D5V 22 D5V H6 H6 H 0 1 N N N 0.315 5.971 8.682 -3.522 1.221 -1.319 H6 D5V 23 D5V H7 H7 H 0 1 N N N -1.262 4.130 7.276 -4.578 -0.549 -0.089 H7 D5V 24 D5V H8 H8 H 0 1 N N N -1.636 5.881 7.417 -3.267 -1.522 -0.823 H8 D5V 25 D5V H9 H9 H 0 1 N N N -2.885 4.661 10.860 -1.886 0.488 2.367 H9 D5V 26 D5V H10 H10 H 0 1 N N N 0.067 1.131 10.841 -1.129 -2.734 -0.068 H10 D5V 27 D5V H11 H11 H 0 1 N N N 2.486 3.396 9.562 0.115 1.148 -2.191 H11 D5V 28 D5V H12 H12 H 0 1 N N N 2.316 4.779 8.711 -1.241 2.112 -2.197 H12 D5V 29 D5V H14 H14 H 0 1 N N N -1.741 -0.214 10.284 1.316 -1.627 0.488 H14 D5V 30 D5V H15 H15 H 0 1 N N N -3.239 -1.943 9.373 3.472 -2.684 -0.053 H15 D5V 31 D5V H16 H16 H 0 1 N N N -5.674 -1.723 9.615 5.450 -1.292 -0.505 H16 D5V 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 D5V C10 O SING N N 1 D5V C10 C9 SING N N 2 D5V O C11 SING N N 3 D5V C9 C8 SING N N 4 D5V C9 O1 SING N N 5 D5V C8 N SING N N 6 D5V C8 C7 SING N N 7 D5V C1 C DOUB Y N 8 D5V C1 C2 SING Y N 9 D5V C C5 SING Y N 10 D5V C11 O1 SING N N 11 D5V C11 C6 SING N N 12 D5V O2 C7 SING N N 13 D5V C6 C7 SING N N 14 D5V C6 S SING N N 15 D5V C2 C3 DOUB Y N 16 D5V C5 C4 DOUB Y N 17 D5V C3 C4 SING Y N 18 D5V C3 S SING N N 19 D5V C4 H1 SING N N 20 D5V C5 H2 SING N N 21 D5V C6 H3 SING N N 22 D5V C7 H4 SING N N 23 D5V C8 H5 SING N N 24 D5V C9 H6 SING N N 25 D5V C10 H7 SING N N 26 D5V C10 H8 SING N N 27 D5V C11 H9 SING N N 28 D5V O2 H10 SING N N 29 D5V N H11 SING N N 30 D5V N H12 SING N N 31 D5V C2 H14 SING N N 32 D5V C1 H15 SING N N 33 D5V C H16 SING N N 34 # # 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 D5V SMILES ACDLabs 12.01 "c1ccccc1SC2C(C(N)C3OC2OC3)O" D5V InChI InChI 1.03 "InChI=1S/C12H15NO3S/c13-9-8-6-15-12(16-8)11(10(9)14)17-7-4-2-1-3-5-7/h1-5,8-12,14H,6,13H2/t8-,9-,10+,11-,12-/m1/s1" D5V InChIKey InChI 1.03 OFCUYBHPAYPQJR-RMPHRYRLSA-N D5V SMILES_CANONICAL CACTVS 3.385 "N[C@@H]1[C@H]2CO[C@H](O2)[C@H](Sc3ccccc3)[C@H]1O" D5V SMILES CACTVS 3.385 "N[CH]1[CH]2CO[CH](O2)[CH](Sc3ccccc3)[CH]1O" D5V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)S[C@@H]2[C@H]([C@@H]([C@H]3CO[C@@H]2O3)N)O" D5V SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)SC2C(C(C3COC2O3)N)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 D5V "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)" D5V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(1~{S},2~{S},3~{S},4~{R},5~{R})-2-azanyl-4-phenylsulfanyl-6,8-dioxabicyclo[3.2.1]octan-3-ol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D5V "Create component" 2017-10-20 RCSB D5V "Initial release" 2020-04-22 RCSB ##