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      ? 
# 
