data_OYD
# 
_chem_comp.id                                    OYD 
_chem_comp.name                                  "6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H20 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-07-18 
_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                        268.312 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OYD 
_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        6PUD 
_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 
OYD C4  C1  C 0 1 N N N N N N 46.662 72.852 225.977 0.790  0.639  -0.082 C4  OYD 1  
OYD C5  C2  C 0 1 N N N N N N 44.899 71.913 227.294 -1.663 0.594  -0.012 C5  OYD 2  
OYD C6  C3  C 0 1 N N N N N N 43.516 71.804 226.707 -2.790 -0.438 -0.087 C6  OYD 3  
OYD C8  C4  C 0 1 N N N N N N 41.071 71.831 227.507 -5.268 -0.759 -0.046 C8  OYD 4  
OYD N1  N1  N 0 1 N N N N N N 45.996 71.720 226.353 -0.370 -0.086 -0.124 N1  OYD 5  
OYD N3  N2  N 0 1 N N N N N N 48.029 75.130 225.351 3.095  2.126  0.006  N3  OYD 6  
OYD C2  C5  C 0 1 N N N N N N 49.261 71.279 224.210 2.902  -2.046 0.391  C2  OYD 7  
OYD O2  O1  O 0 1 N N N N N N 46.426 76.338 226.376 1.831  3.924  0.241  O2  OYD 8  
OYD N   N3  N 0 1 N N N N N N 48.177 71.492 224.873 2.098  -1.356 -0.347 N   OYD 9  
OYD C   C6  C 0 1 N N N N N N 48.903 68.869 224.800 4.325  -4.038 -0.003 C   OYD 10 
OYD C1  C7  C 0 1 N N N N N N 49.550 69.879 223.893 2.906  -3.550 0.298  C1  OYD 11 
OYD C10 C8  C 0 1 N N N N N N 46.870 75.250 226.064 1.892  2.717  0.105  C10 OYD 12 
OYD C11 C9  C 0 1 N N N N N N 48.577 73.964 224.866 3.199  0.791  -0.146 C11 OYD 13 
OYD C3  C10 C 0 1 N N N N N N 47.819 72.792 225.198 2.023  0.003  -0.194 C3  OYD 14 
OYD C7  C11 C 0 1 N N N N N N 42.531 72.052 227.870 -4.141 0.273  0.030  C7  OYD 15 
OYD C9  C12 C 0 1 N N N N N N 40.126 72.430 228.550 -6.618 -0.049 0.072  C9  OYD 16 
OYD N2  N4  N 0 1 N N N N N N 46.222 74.080 226.376 0.753  2.003  0.064  N2  OYD 17 
OYD O1  O2  O 0 1 N N N N N N 40.222 73.835 228.408 -7.671 -1.013 0.001  O1  OYD 18 
OYD O3  O3  O 0 1 N N N N N N 49.618 74.001 224.226 4.295  0.267  -0.240 O3  OYD 19 
OYD H1  H1  H 0 1 N N N N N N 44.993 71.154 228.084 -1.770 1.309  -0.828 H1  OYD 20 
OYD H2  H2  H 0 1 N N N N N N 45.002 72.916 227.734 -1.716 1.120  0.941  H2  OYD 21 
OYD H3  H3  H 0 1 N N N N N N 43.375 72.560 225.921 -2.738 -0.964 -1.040 H3  OYD 22 
OYD H4  H4  H 0 1 N N N N N N 43.360 70.801 226.283 -2.684 -1.152 0.729  H4  OYD 23 
OYD H5  H5  H 0 1 N N N N N N 40.871 72.303 226.534 -5.215 -1.285 -0.999 H5  OYD 24 
OYD H6  H6  H 0 1 N N N N N N 40.882 70.750 227.436 -5.161 -1.474 0.770  H6  OYD 25 
OYD H7  H7  H 0 1 N N N N N N 45.622 71.296 225.528 -0.337 -1.049 -0.228 H7  OYD 26 
OYD H8  H8  H 0 1 N N N N N N 48.530 75.975 225.162 3.899  2.668  0.039  H8  OYD 27 
OYD H9  H9  H 0 1 N N N N N N 49.916 72.083 223.907 3.570  -1.545 1.075  H9  OYD 28 
OYD H10 H10 H 0 1 N N N N N N 49.182 67.855 224.478 4.328  -5.126 -0.071 H10 OYD 29 
OYD H11 H11 H 0 1 N N N N N N 49.244 69.033 225.833 4.661  -3.615 -0.949 H11 OYD 30 
OYD H12 H12 H 0 1 N N N N N N 47.810 68.981 224.753 4.995  -3.721 0.796  H12 OYD 31 
OYD H13 H13 H 0 1 N N N N N N 49.205 69.685 222.867 2.570  -3.974 1.244  H13 OYD 32 
OYD H14 H14 H 0 1 N N N N N N 50.639 69.736 223.947 2.236  -3.867 -0.501 H14 OYD 33 
OYD H16 H16 H 0 1 N N N N N N 42.789 71.369 228.693 -4.193 0.799  0.983  H16 OYD 34 
OYD H17 H17 H 0 1 N N N N N N 42.649 73.093 228.207 -4.247 0.987  -0.786 H17 OYD 35 
OYD H18 H18 H 0 1 N N N N N N 39.094 72.098 228.365 -6.670 0.477  1.025  H18 OYD 36 
OYD H19 H19 H 0 1 N N N N N N 40.433 72.127 229.562 -6.725 0.666  -0.744 H19 OYD 37 
OYD H20 H20 H 0 1 N N N N N N 39.650 74.257 229.038 -8.557 -0.633 0.069  H20 OYD 38 
OYD H15 H15 H 0 1 N N N N N N 45.386 74.131 226.923 -0.102 2.455  0.138  H15 OYD 39 
# 
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 
OYD C1  C2  SING N N 1  
OYD C1  C   SING N N 2  
OYD C2  N   DOUB N N 3  
OYD O3  C11 DOUB N N 4  
OYD C11 C3  SING N N 5  
OYD C11 N3  SING N N 6  
OYD N   C3  SING N N 7  
OYD C3  C4  DOUB N N 8  
OYD N3  C10 SING N N 9  
OYD C4  N1  SING N N 10 
OYD C4  N2  SING N N 11 
OYD C10 N2  SING N N 12 
OYD C10 O2  DOUB N N 13 
OYD N1  C5  SING N N 14 
OYD C6  C5  SING N N 15 
OYD C6  C7  SING N N 16 
OYD C8  C7  SING N N 17 
OYD C8  C9  SING N N 18 
OYD O1  C9  SING N N 19 
OYD C5  H1  SING N N 20 
OYD C5  H2  SING N N 21 
OYD C6  H3  SING N N 22 
OYD C6  H4  SING N N 23 
OYD C8  H5  SING N N 24 
OYD C8  H6  SING N N 25 
OYD N1  H7  SING N N 26 
OYD N3  H8  SING N N 27 
OYD C2  H9  SING N N 28 
OYD C   H10 SING N N 29 
OYD C   H11 SING N N 30 
OYD C   H12 SING N N 31 
OYD C1  H13 SING N N 32 
OYD C1  H14 SING N N 33 
OYD C7  H16 SING N N 34 
OYD C7  H17 SING N N 35 
OYD C9  H18 SING N N 36 
OYD C9  H19 SING N N 37 
OYD O1  H20 SING N N 38 
OYD N2  H15 SING N N 39 
# 
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 
OYD SMILES           ACDLabs              12.01 "C=1(NCCCCCO)NC(NC(C=1N=[C@H]CC)=O)=O"                                                                                   
OYD InChI            InChI                1.03  "InChI=1S/C12H20N4O3/c1-2-6-13-9-10(14-7-4-3-5-8-17)15-12(19)16-11(9)18/h6,17H,2-5,7-8H2,1H3,(H3,14,15,16,18,19)/b13-6+" 
OYD InChIKey         InChI                1.03  ZKFUQHLXTDAXLG-AWNIVKPZSA-N                                                                                              
OYD SMILES_CANONICAL CACTVS               3.385 "CCC=NC1=C(NCCCCCO)NC(=O)NC1=O"                                                                                          
OYD SMILES           CACTVS               3.385 "CCC=NC1=C(NCCCCCO)NC(=O)NC1=O"                                                                                          
OYD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC/C=N/C1=C(NC(=O)NC1=O)NCCCCCO"                                                                                        
OYD SMILES           "OpenEye OEToolkits" 2.0.7 "CCC=NC1=C(NC(=O)NC1=O)NCCCCCO"                                                                                          
# 
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 
OYD "SYSTEMATIC NAME" ACDLabs              12.01 "6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione"   
OYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "6-(5-oxidanylpentylamino)-5-[(~{E})-propylideneamino]-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 
OYD "Create component"   2019-07-18 RCSB 
OYD "Other modification" 2019-09-30 RCSB 
OYD "Initial release"    2020-02-19 RCSB 
OYD "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            OYD 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_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               C1 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
