data_YC6 # _chem_comp.id YC6 _chem_comp.name "1-(2-deoxy-alpha-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H12 N2 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-30 _chem_comp.pdbx_modified_date 2025-05-02 _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 256.212 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YC6 _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 8V4E _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_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 YC6 N N1 N 0 1 N N N N N N -46.216 38.837 190.739 -0.436 0.549 0.491 N YC6 1 YC6 C C1 C 0 1 N N N N N N -49.139 38.749 193.082 -2.790 -2.214 -0.290 C YC6 2 YC6 C1 C2 C 0 1 N N N N N N -48.057 39.223 192.231 -2.244 -0.881 -0.045 C1 YC6 3 YC6 C2 C3 C 0 1 N N N N N N -47.232 38.384 191.552 -0.906 -0.705 0.270 C2 YC6 4 YC6 C3 C4 C 0 1 N N S N N N -45.368 37.888 189.984 0.979 0.734 0.823 C3 YC6 5 YC6 C4 C5 C 0 1 N N N N N N -46.151 36.792 189.275 1.656 1.622 -0.243 C4 YC6 6 YC6 C5 C6 C 0 1 N N S N N N -45.659 35.472 189.857 3.044 0.945 -0.403 C5 YC6 7 YC6 C6 C7 C 0 1 N N R N N N -44.884 35.887 191.102 2.672 -0.544 -0.188 C6 YC6 8 YC6 C7 C8 C 0 1 N N N N N N -43.656 35.052 191.366 3.890 -1.330 0.301 C7 YC6 9 YC6 C8 C9 C 0 1 N N N N N N -45.974 40.187 190.575 -1.235 1.623 0.406 C8 YC6 10 YC6 C9 C10 C 0 1 N N N N N N -47.858 40.661 192.100 -3.097 0.317 -0.135 C9 YC6 11 YC6 N1 N2 N 0 1 N N N N N N -46.815 41.020 191.271 -2.540 1.524 0.101 N1 YC6 12 YC6 O1 O1 O 0 1 N N N N N N -46.773 34.658 190.228 3.574 1.159 -1.713 O1 YC6 13 YC6 O2 O2 O 0 1 N N N N N N -42.732 35.136 190.290 3.560 -2.718 0.383 O2 YC6 14 YC6 O3 O3 O 0 1 N N N N N N -44.488 37.257 190.896 1.649 -0.533 0.820 O3 YC6 15 YC6 O4 O4 O 0 1 N N N N N N -45.081 40.619 189.860 -0.763 2.724 0.614 O4 YC6 16 YC6 O5 O5 O 0 1 N N N N N N -48.533 41.528 192.652 -4.277 0.222 -0.417 O5 YC6 17 YC6 H1 H1 H 0 1 N N N N N N -49.899 39.013 192.362 -2.149 -3.081 -0.227 H1 YC6 18 YC6 H4 H4 H 0 1 N N N N N N -47.378 37.319 191.654 -0.244 -1.556 0.339 H4 YC6 19 YC6 H5 H5 H 0 1 N N N N N N -44.790 38.445 189.232 1.071 1.198 1.805 H5 YC6 20 YC6 H6 H6 H 0 1 N N N N N N -45.959 36.826 188.192 1.100 1.594 -1.181 H6 YC6 21 YC6 H7 H7 H 0 1 N N N N N N -47.229 36.912 189.461 1.762 2.645 0.115 H7 YC6 22 YC6 H8 H8 H 0 1 N N N N N N -44.996 34.960 189.144 3.740 1.291 0.361 H8 YC6 23 YC6 H9 H9 H 0 1 N N N N N N -45.554 35.820 191.972 2.290 -0.976 -1.113 H9 YC6 24 YC6 H10 H10 H 0 1 N N N N N N -43.958 34.002 191.497 4.716 -1.194 -0.397 H10 YC6 25 YC6 H11 H11 H 0 1 N N N N N N -43.169 35.411 192.285 4.185 -0.969 1.287 H11 YC6 26 YC6 H12 H12 H 0 1 N N N N N N -46.653 42.001 191.165 -3.085 2.325 0.049 H12 YC6 27 YC6 H13 H13 H 0 1 N N N N N N -46.460 33.837 190.590 3.721 2.089 -1.931 H13 YC6 28 YC6 H14 H14 H 0 1 N N N N N N -41.971 34.602 190.483 4.287 -3.279 0.687 H14 YC6 29 YC6 O6 O6 O 0 1 N N N N N N -50.094 38.246 194.020 -3.965 -2.348 -0.564 O6 YC6 30 # 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 YC6 C4 C5 SING N N 1 YC6 C4 C3 SING N N 2 YC6 C5 O1 SING N N 3 YC6 C5 C6 SING N N 4 YC6 O4 C8 DOUB N N 5 YC6 C3 N SING N N 6 YC6 C3 O3 SING N N 7 YC6 O2 C7 SING N N 8 YC6 C8 N SING N N 9 YC6 C8 N1 SING N N 10 YC6 N C2 SING N N 11 YC6 O3 C6 SING N N 12 YC6 C6 C7 SING N N 13 YC6 N1 C9 SING N N 14 YC6 C2 C1 DOUB N N 15 YC6 C9 C1 SING N N 16 YC6 C9 O5 DOUB N N 17 YC6 C1 C SING N N 18 YC6 C H1 SING N N 19 YC6 C2 H4 SING N N 20 YC6 C3 H5 SING N N 21 YC6 C4 H6 SING N N 22 YC6 C4 H7 SING N N 23 YC6 C5 H8 SING N N 24 YC6 C6 H9 SING N N 25 YC6 C7 H10 SING N N 26 YC6 C7 H11 SING N N 27 YC6 N1 H12 SING N N 28 YC6 O1 H13 SING N N 29 YC6 O2 H14 SING N N 30 YC6 C O6 DOUB N N 31 # 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 YC6 SMILES ACDLabs 12.01 "O=CC1=CN(C(=O)NC1=O)C1CC(O)C(CO)O1" YC6 InChI InChI 1.06 "InChI=1S/C10H12N2O6/c13-3-5-2-12(10(17)11-9(5)16)8-1-6(15)7(4-14)18-8/h2-3,6-8,14-15H,1,4H2,(H,11,16,17)/t6-,7+,8-/m0/s1" YC6 InChIKey InChI 1.06 MVORBLZUGBSUNB-RNJXMRFFSA-N YC6 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@@H](C[C@@H]1O)N2C=C(C=O)C(=O)NC2=O" YC6 SMILES CACTVS 3.385 "OC[CH]1O[CH](C[CH]1O)N2C=C(C=O)C(=O)NC2=O" YC6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@@H]1N2C=C(C(=O)NC2=O)C=O)CO)O" YC6 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1N2C=C(C(=O)NC2=O)C=O)CO)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 YC6 "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-alpha-D-erythro-pentofuranosyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde" YC6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{S},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidine-5-carbaldehyde" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YC6 "Create component" 2023-11-30 RCSB YC6 "Modify coordinates" 2023-12-05 RCSB YC6 "Modify PCM" 2024-09-27 PDBE YC6 "Initial release" 2025-05-07 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YC6 _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 C _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 ? #