data_Y3G
# 
_chem_comp.id                                    Y3G 
_chem_comp.name                                  "5-ethynylpyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C6 H4 N2 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-02-01 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        136.108 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3G 
_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        7LJU 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
Y3G C10 C1 C 0 1 N N N N N N 20.704 39.162 47.578 -3.517 -0.533 0.001  C10 Y3G 1  
Y3G C01 C2 C 0 1 N N N N N N 23.099 41.849 48.314 -0.257 0.969  0.002  C01 Y3G 2  
Y3G C03 C3 C 0 1 N N N N N N 24.420 42.116 50.201 1.810  -0.122 0.000  C03 Y3G 3  
Y3G C05 C4 C 0 1 N N N N N N 23.000 40.264 50.076 -0.134 -1.463 -0.001 C05 Y3G 4  
Y3G C06 C5 C 0 1 N N N N N N 22.564 40.672 48.836 -0.918 -0.344 0.000  C06 Y3G 5  
Y3G C09 C6 C 0 1 N N N N N N 21.526 39.820 48.125 -2.346 -0.448 0.000  C09 Y3G 6  
Y3G N02 N1 N 0 1 N N N N N N 24.011 42.547 48.998 1.092  1.015  0.002  N02 Y3G 7  
Y3G N04 N2 N 0 1 N N N N N N 23.918 40.983 50.716 1.225  -1.330 -0.001 N04 Y3G 8  
Y3G O07 O1 O 0 1 N N N N N N 25.247 42.732 50.820 3.024  -0.053 -0.000 O07 Y3G 9  
Y3G O08 O2 O 0 1 N N N N N N 22.764 42.270 47.255 -0.913 1.994  -0.002 O08 Y3G 10 
Y3G H1  H1 H 0 1 N N N N N N 19.970 38.574 47.089 -4.564 -0.610 0.001  H1  Y3G 11 
Y3G H2  H2 H 0 1 N N N N N N 22.600 39.367 50.526 -0.585 -2.444 -0.001 H2  Y3G 12 
Y3G H4  H4 H 0 1 N N N N N N 24.388 43.390 48.613 1.546  1.872  0.003  H4  Y3G 13 
Y3G H3  H3 H 0 1 N N N N N N 24.244 40.670 51.608 1.779  -2.126 -0.002 H3  Y3G 14 
# 
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 
Y3G O08 C01 DOUB N N 1  
Y3G C10 C09 TRIP N N 2  
Y3G C09 C06 SING N N 3  
Y3G C01 C06 SING N N 4  
Y3G C01 N02 SING N N 5  
Y3G C06 C05 DOUB N N 6  
Y3G N02 C03 SING N N 7  
Y3G C05 N04 SING N N 8  
Y3G C03 N04 SING N N 9  
Y3G C03 O07 DOUB N N 10 
Y3G C10 H1  SING N N 11 
Y3G C05 H2  SING N N 12 
Y3G N02 H4  SING N N 13 
Y3G N04 H3  SING N N 14 
# 
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 
Y3G SMILES           ACDLabs              12.01 "C#CC=1C(NC(NC=1)=O)=O"                                         
Y3G InChI            InChI                1.03  "InChI=1S/C6H4N2O2/c1-2-4-3-7-6(10)8-5(4)9/h1,3H,(H2,7,8,9,10)" 
Y3G InChIKey         InChI                1.03  JOZGNYDSEBIJDH-UHFFFAOYSA-N                                     
Y3G SMILES_CANONICAL CACTVS               3.385 "O=C1NC=C(C#C)C(=O)N1"                                          
Y3G SMILES           CACTVS               3.385 "O=C1NC=C(C#C)C(=O)N1"                                          
Y3G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CC1=CNC(=O)NC1=O"                                            
Y3G SMILES           "OpenEye OEToolkits" 2.0.7 "C#CC1=CNC(=O)NC1=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 
Y3G "SYSTEMATIC NAME" ACDLabs              12.01 "5-ethynylpyrimidine-2,4(1H,3H)-dione" 
Y3G "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-ethynyl-1~{H}-pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3G "Create component" 2021-02-01 RCSB 
Y3G "Initial release"  2021-04-07 RCSB 
Y3G "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y3G 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C09 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
