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 ? #