data_YRD # _chem_comp.id YRD _chem_comp.name "~{N}-(4-methyl-5-oxidanylidene-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H16 N2 O2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-12-12 _chem_comp.pdbx_modified_date 2024-10-11 _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 284.398 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YRD _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 8RDO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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 YRD C4 C1 C 0 1 N N N N N N 8.022 66.693 36.575 -2.859 0.166 -0.042 C4 YRD 1 YRD C6 C2 C 0 1 N N N N N N 9.742 65.377 36.557 -2.151 -1.979 -0.003 C6 YRD 2 YRD C8 C3 C 0 1 N N N N N N 8.773 64.708 35.932 -1.028 -1.172 0.073 C8 YRD 3 YRD C10 C4 C 0 1 N N N N N N 8.327 62.974 34.379 1.320 -0.715 0.096 C10 YRD 4 YRD C13 C5 C 0 1 N N N N N N 8.430 59.706 32.287 5.138 -0.464 -0.030 C13 YRD 5 YRD C15 C6 C 0 1 N N N N N N 8.351 58.035 30.398 7.527 0.261 -0.129 C15 YRD 6 YRD C17 C7 C 0 1 N N N N N N 7.679 65.508 35.947 -1.468 0.163 0.046 C17 YRD 7 YRD O7 O1 O 0 1 N N N N N N 10.891 64.975 36.756 -2.146 -3.203 -0.007 O7 YRD 8 YRD N5 N1 N 0 1 N N N N N N 9.296 66.555 36.930 -3.241 -1.208 -0.074 N5 YRD 9 YRD C18 C8 C 0 1 N N N N N N 10.085 67.521 37.659 -4.618 -1.699 -0.169 C18 YRD 10 YRD C3 C9 C 0 1 N N N N N N 7.122 67.701 36.722 -3.586 1.309 -0.087 C3 YRD 11 YRD S2 S1 S 0 1 N N N N N N 5.595 67.423 36.098 -2.661 2.745 -0.018 S2 YRD 12 YRD S1 S2 S 0 1 N N N N N N 6.007 65.523 35.383 -0.819 1.810 0.089 S1 YRD 13 YRD N9 N2 N 0 1 N N N N N N 8.949 63.448 35.484 0.313 -1.610 0.158 N9 YRD 14 YRD O16 O2 O 0 1 N N N N N N 7.628 63.643 33.621 1.074 0.473 0.064 O16 YRD 15 YRD C11 C10 C 0 1 N N N N N N 8.612 61.492 34.069 2.750 -1.190 0.068 C11 YRD 16 YRD C12 C11 C 0 1 N N N N N N 8.067 61.141 32.676 3.687 0.018 -0.002 C12 YRD 17 YRD C14 C12 C 0 1 N N N N N N 8.017 59.465 30.836 6.076 0.743 -0.100 C14 YRD 18 YRD H2 H2 H 0 1 N N N N N N 7.900 59.000 32.944 5.349 -1.036 0.873 H2 YRD 19 YRD H3 H3 H 0 1 N N N N N N 9.515 59.559 32.391 5.294 -1.096 -0.905 H3 YRD 20 YRD H4 H4 H 0 1 N N N N N N 8.043 57.890 29.352 8.195 1.121 -0.178 H4 YRD 21 YRD H5 H5 H 0 1 N N N N N N 9.434 57.868 30.488 7.738 -0.311 0.775 H5 YRD 22 YRD H6 H6 H 0 1 N N N N N N 7.815 57.320 31.040 7.683 -0.371 -1.003 H6 YRD 23 YRD H7 H7 H 0 1 N N N N N N 9.481 68.421 37.848 -4.890 -1.817 -1.218 H7 YRD 24 YRD H8 H8 H 0 1 N N N N N N 10.403 67.086 38.618 -4.697 -2.661 0.337 H8 YRD 25 YRD H9 H9 H 0 1 N N N N N N 10.972 67.792 37.067 -5.292 -0.984 0.303 H9 YRD 26 YRD H10 H10 H 0 1 N N N N N N 7.378 68.628 37.213 -4.663 1.313 -0.161 H10 YRD 27 YRD H11 H11 H 0 1 N N N N N N 9.563 62.840 35.988 0.509 -2.554 0.260 H11 YRD 28 YRD H12 H12 H 0 1 N N N N N N 8.122 60.860 34.824 2.960 -1.762 0.972 H12 YRD 29 YRD H13 H13 H 0 1 N N N N N N 9.698 61.316 34.092 2.905 -1.821 -0.806 H13 YRD 30 YRD H14 H14 H 0 1 N N N N N N 8.497 61.833 31.937 3.531 0.650 0.873 H14 YRD 31 YRD H15 H15 H 0 1 N N N N N N 6.972 61.245 32.682 3.476 0.590 -0.905 H15 YRD 32 YRD H16 H16 H 0 1 N N N N N N 8.553 60.174 30.187 5.865 1.315 -1.004 H16 YRD 33 YRD H17 H17 H 0 1 N N N N N N 6.933 59.627 30.739 5.920 1.375 0.775 H17 YRD 34 # 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 YRD C15 C14 SING N N 1 YRD C14 C13 SING N N 2 YRD C13 C12 SING N N 3 YRD C12 C11 SING N N 4 YRD O16 C10 DOUB N N 5 YRD C11 C10 SING N N 6 YRD C10 N9 SING N N 7 YRD S1 C17 SING N N 8 YRD S1 S2 SING N N 9 YRD N9 C8 SING N N 10 YRD C8 C17 DOUB N N 11 YRD C8 C6 SING N N 12 YRD C17 C4 SING N N 13 YRD S2 C3 SING N N 14 YRD C6 O7 DOUB N N 15 YRD C6 N5 SING N N 16 YRD C4 C3 DOUB N N 17 YRD C4 N5 SING N N 18 YRD N5 C18 SING N N 19 YRD C13 H2 SING N N 20 YRD C13 H3 SING N N 21 YRD C15 H4 SING N N 22 YRD C15 H5 SING N N 23 YRD C15 H6 SING N N 24 YRD C18 H7 SING N N 25 YRD C18 H8 SING N N 26 YRD C18 H9 SING N N 27 YRD C3 H10 SING N N 28 YRD N9 H11 SING N N 29 YRD C11 H12 SING N N 30 YRD C11 H13 SING N N 31 YRD C12 H14 SING N N 32 YRD C12 H15 SING N N 33 YRD C14 H16 SING N N 34 YRD C14 H17 SING N N 35 # 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 YRD InChI InChI 1.06 "InChI=1S/C12H16N2O2S2/c1-3-4-5-6-9(15)13-10-11-8(7-17-18-11)14(2)12(10)16/h7H,3-6H2,1-2H3,(H,13,15)" YRD InChIKey InChI 1.06 ZXLPBBAXZZCKNU-UHFFFAOYSA-N YRD SMILES_CANONICAL CACTVS 3.385 "CCCCCC(=O)NC1=C2SSC=C2N(C)C1=O" YRD SMILES CACTVS 3.385 "CCCCCC(=O)NC1=C2SSC=C2N(C)C1=O" YRD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCC(=O)NC1=C2C(=CSS2)N(C1=O)C" YRD SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCC(=O)NC1=C2C(=CSS2)N(C1=O)C" # _pdbx_chem_comp_identifier.comp_id YRD _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "~{N}-(4-methyl-5-oxidanylidene-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YRD "Create component" 2023-12-12 PDBE YRD "Initial release" 2024-10-16 RCSB #