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 
# 
