data_OYV
# 
_chem_comp.id                                    OYV 
_chem_comp.name                                  "1,2-dideoxy-1-{2,6-dioxo-5-[(1E)-3-oxobut-1-en-1-yl]-1,2,3,6-tetrahydropyrimidin-4-yl}-D-ribo-hexitol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H20 N2 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-07-19 
_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                        328.318 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OYV 
_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        6PUK 
_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 
OYV C1  C1  C 0 1 N N N N N N -48.009 36.939 192.226 2.776  -3.473 -0.266 C1  OYV 1  
OYV C2  C2  C 0 1 N N N N N N -47.324 38.196 191.884 3.073  -2.108 -0.133 C2  OYV 2  
OYV C3  C3  C 0 1 N N N N N N -46.277 38.331 191.072 2.109  -1.177 -0.361 C3  OYV 3  
OYV C4  C4  C 0 1 N N N N N N -45.712 39.601 190.640 2.396  0.241  -0.148 C4  OYV 4  
OYV C5  C5  C 0 1 N N N N N N -44.502 39.558 189.975 1.468  1.215  -0.481 C5  OYV 5  
OYV C6  C6  C 0 1 N N N N N N -43.722 38.317 189.665 0.139  0.829  -1.077 C6  OYV 6  
OYV C7  C7  C 0 1 N N N N N N -42.908 38.415 188.370 -0.909 0.731  0.033  C7  OYV 7  
OYV C8  C8  C 0 1 N N S N N N -41.397 38.473 188.593 -2.259 0.339  -0.572 C8  OYV 8  
OYV C9  C9  C 0 1 N N S N N N -40.878 39.840 189.042 -3.276 0.120  0.549  C9  OYV 9  
OYV C10 C10 C 0 1 N N R N N N -39.354 39.954 189.023 -4.625 -0.272 -0.056 C10 OYV 10 
OYV C11 C11 C 0 1 N N N N N N -38.795 39.575 187.661 -5.643 -0.491 1.066  C11 OYV 11 
OYV N   N1  N 0 1 N N N N N N -43.951 40.741 189.545 1.770  2.521  -0.264 N   OYV 12 
OYV C   C12 C 0 1 N N N N N N -47.522 35.652 191.626 3.844  -4.505 -0.008 C   OYV 13 
OYV C12 C13 C 0 1 N N N N N N -44.534 41.966 189.733 2.946  2.891  0.266  C12 OYV 14 
OYV C13 C14 C 0 1 N N N N N N -46.391 40.855 190.883 3.679  0.677  0.432  C13 OYV 15 
OYV N1  N2  N 0 1 N N N N N N -45.729 41.960 190.397 3.889  1.998  0.611  N1  OYV 16 
OYV O1  O1  O 0 1 N N N N N N -40.995 37.466 189.523 -2.716 1.384  -1.433 O1  OYV 17 
OYV O2  O2  O 0 1 N N N N N N -41.416 40.849 188.188 -2.818 -0.925 1.410  O2  OYV 18 
OYV O3  O3  O 0 1 N N N N N N -38.994 41.308 189.298 -5.083 0.773  -0.916 O3  OYV 19 
OYV O4  O4  O 0 1 N N N N N N -37.490 40.109 187.486 -6.869 -0.970 0.510  O4  OYV 20 
OYV O5  O5  O 0 1 N N N N N N -44.024 43.004 189.324 3.166  4.074  0.439  O5  OYV 21 
OYV O6  O6  O 0 1 N N N N N N -47.458 41.004 191.465 4.527  -0.136 0.748  O6  OYV 22 
OYV H3  H3  H 0 1 N N N N N N -47.708 39.098 192.336 4.068  -1.796 0.149  H3  OYV 23 
OYV H4  H4  H 0 1 N N N N N N -45.811 37.428 190.706 1.130  -1.485 -0.698 H4  OYV 24 
OYV H6  H6  H 0 1 N N N N N N -44.426 37.477 189.571 -0.168 1.584  -1.801 H6  OYV 25 
OYV H7  H7  H 0 1 N N N N N N -43.030 38.124 190.498 0.231  -0.136 -1.576 H7  OYV 26 
OYV H8  H8  H 0 1 N N N N N N -43.215 39.326 187.836 -0.602 -0.024 0.757  H8  OYV 27 
OYV H9  H9  H 0 1 N N N N N N -43.134 37.534 187.751 -1.001 1.696  0.532  H9  OYV 28 
OYV H10 H10 H 0 1 N N N N N N -40.923 38.254 187.625 -2.146 -0.581 -1.145 H10 OYV 29 
OYV H11 H11 H 0 1 N N N N N N -41.220 40.013 190.073 -3.388 1.040  1.123  H11 OYV 30 
OYV H12 H12 H 0 1 N N N N N N -38.934 39.282 189.786 -4.513 -1.192 -0.629 H12 OYV 31 
OYV H13 H13 H 0 1 N N N N N N -39.456 39.972 186.876 -5.253 -1.225 1.771  H13 OYV 32 
OYV H14 H14 H 0 1 N N N N N N -38.750 38.479 187.582 -5.822 0.451  1.583  H14 OYV 33 
OYV H15 H15 H 0 1 N N N N N N -48.090 34.811 192.050 3.429  -5.502 -0.154 H15 OYV 34 
OYV H16 H16 H 0 1 N N N N N N -47.666 35.678 190.536 4.672  -4.351 -0.699 H16 OYV 35 
OYV H17 H17 H 0 1 N N N N N N -46.453 35.524 191.852 4.203  -4.407 1.017  H17 OYV 36 
OYV H18 H18 H 0 1 N N N N N N -46.166 42.847 190.545 4.727  2.306  0.991  H18 OYV 37 
OYV H19 H19 H 0 1 N N N N N N -40.055 37.512 189.653 -2.839 2.234  -0.988 H19 OYV 38 
OYV H20 H20 H 0 1 N N N N N N -41.097 41.700 188.463 -2.696 -1.775 0.966  H20 OYV 39 
OYV H21 H21 H 0 1 N N N N N N -39.336 41.561 190.147 -5.206 1.623  -0.472 H21 OYV 40 
OYV H22 H22 H 0 1 N N N N N N -37.158 39.862 186.631 -7.562 -1.131 1.165  H22 OYV 41 
OYV O7  O7  O 0 1 N N N N N N -48.840 35.975 192.878 1.657  -3.823 -0.583 O7  OYV 42 
OYV H1  H1  H 0 1 N N N N N N -43.073 40.705 189.067 1.120  3.203  -0.497 H1  OYV 43 
# 
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 
OYV O4  C11 SING N N 1  
OYV C11 C10 SING N N 2  
OYV O2  C9  SING N N 3  
OYV C7  C8  SING N N 4  
OYV C7  C6  SING N N 5  
OYV C8  C9  SING N N 6  
OYV C8  O1  SING N N 7  
OYV C10 C9  SING N N 8  
OYV C10 O3  SING N N 9  
OYV O5  C12 DOUB N N 10 
OYV N   C12 SING N N 11 
OYV N   C5  SING N N 12 
OYV C6  C5  SING N N 13 
OYV C12 N1  SING N N 14 
OYV C5  C4  DOUB N N 15 
OYV N1  C13 SING N N 16 
OYV C4  C13 SING N N 17 
OYV C4  C3  SING N N 18 
OYV C13 O6  DOUB N N 19 
OYV C3  C2  DOUB N E 20 
OYV C   C1  SING N N 21 
OYV C2  C1  SING N N 22 
OYV C2  H3  SING N N 23 
OYV C3  H4  SING N N 24 
OYV C6  H6  SING N N 25 
OYV C6  H7  SING N N 26 
OYV C7  H8  SING N N 27 
OYV C7  H9  SING N N 28 
OYV C8  H10 SING N N 29 
OYV C9  H11 SING N N 30 
OYV C10 H12 SING N N 31 
OYV C11 H13 SING N N 32 
OYV C11 H14 SING N N 33 
OYV C   H15 SING N N 34 
OYV C   H16 SING N N 35 
OYV C   H17 SING N N 36 
OYV N1  H18 SING N N 37 
OYV O1  H19 SING N N 38 
OYV O2  H20 SING N N 39 
OYV O3  H21 SING N N 40 
OYV O4  H22 SING N N 41 
OYV C1  O7  DOUB N N 42 
OYV N   H1  SING N N 43 
# 
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 
OYV SMILES           ACDLabs              12.01 "C(=O)([C@H]=[C@H]C=1C(=O)NC(NC=1CCC(C(C(O)CO)O)O)=O)C"                                                                                                       
OYV InChI            InChI                1.03  "InChI=1S/C14H20N2O7/c1-7(18)2-3-8-9(15-14(23)16-13(8)22)4-5-10(19)12(21)11(20)6-17/h2-3,10-12,17,19-21H,4-6H2,1H3,(H2,15,16,22,23)/b3-2+/t10-,11+,12-/m0/s1" 
OYV InChIKey         InChI                1.03  YIGUGMFHMVTCHU-VUGGRDAHSA-N                                                                                                                                   
OYV SMILES_CANONICAL CACTVS               3.385 "CC(=O)/C=C/C1=C(CC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O"                                                                                                    
OYV SMILES           CACTVS               3.385 "CC(=O)C=CC1=C(CC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O"                                                                                                         
OYV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)/C=C/C1=C(NC(=O)NC1=O)CC[C@@H]([C@@H]([C@@H](CO)O)O)O"                                                                                                 
OYV SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C=CC1=C(NC(=O)NC1=O)CCC(C(C(CO)O)O)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 
OYV "SYSTEMATIC NAME" ACDLabs              12.01 "1,2-dideoxy-1-{2,6-dioxo-5-[(1E)-3-oxobut-1-en-1-yl]-1,2,3,6-tetrahydropyrimidin-4-yl}-D-ribo-hexitol"                   
OYV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[(~{E})-3-oxidanylidenebut-1-enyl]-6-[(3~{S},4~{S},5~{R})-3,4,5,6-tetrakis(oxidanyl)hexyl]-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 
OYV "Create component"   2019-07-19 RCSB 
OYV "Other modification" 2019-10-02 RCSB 
OYV "Initial release"    2020-02-19 RCSB 
OYV "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            OYV 
_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      ? 
# 
