data_Q84
# 
_chem_comp.id                                    Q84 
_chem_comp.name                                  "1,2-dideoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-erythro-pentitol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H18 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-10-02 
_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                        314.295 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Q84 
_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        6PUM 
_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 
Q84 C   C1  C 0 1 N N N N N N -0.648 30.425 255.163 4.554  3.914  0.795  C   Q84 1  
Q84 N   N1  N 0 1 N N N N N N 0.434  27.810 255.161 2.521  1.038  -0.424 N   Q84 2  
Q84 C1  C2  C 0 1 N N N N N N 0.564  30.009 255.958 3.582  3.102  -0.022 C1  Q84 3  
Q84 C10 C3  C 0 1 N N N N N N 1.663  23.986 254.047 2.152  -2.976 0.254  C10 Q84 4  
Q84 C11 C4  C 0 1 N N N N N N 2.217  26.036 255.291 3.574  -1.149 -0.093 C11 Q84 5  
Q84 C2  C5  C 0 1 N N N N N N 1.164  28.698 255.729 3.366  1.743  0.286  C2  Q84 6  
Q84 C3  C6  C 0 1 N N N N N N 0.928  26.528 254.917 2.393  -0.280 -0.201 C3  Q84 7  
Q84 C4  C7  C 0 1 N N N N N N 0.075  25.807 254.090 1.125  -0.875 -0.064 C4  Q84 8  
Q84 C5  C8  C 0 1 N N N N N N -1.868 25.686 252.591 -1.320 -0.754 -0.009 C5  Q84 9  
Q84 C6  C9  C 0 1 N N N N N N -3.025 24.833 253.042 -2.414 0.306  -0.152 C6  Q84 10 
Q84 C7  C10 C 0 1 N N S N N N -2.589 23.436 253.418 -3.786 -0.353 -0.001 C7  Q84 11 
Q84 C8  C11 C 0 1 N N R N N N -3.745 22.445 253.407 -4.874 0.722  -0.019 C8  Q84 12 
Q84 C9  C12 C 0 1 N N N N N N -4.311 22.268 252.008 -6.246 0.063  0.133  C9  Q84 13 
Q84 N1  N2  N 0 1 N N N N N N -1.124 26.336 253.661 -0.006 -0.122 -0.154 N1  Q84 14 
Q84 N2  N3  N 0 1 N N N N N N 0.454  24.554 253.704 1.048  -2.220 0.162  N2  Q84 15 
Q84 N3  N4  N 0 1 N N N N N N 2.495  24.766 254.801 3.388  -2.466 0.131  N3  Q84 16 
Q84 O1  O1  O 0 1 N N N N N N -1.528 22.977 252.567 -3.999 -1.264 -1.081 O1  Q84 17 
Q84 O2  O2  O 0 1 N N N N N N -3.287 21.196 253.905 -4.661 1.633  1.061  O2  Q84 18 
Q84 O3  O3  O 0 1 N N N N N N -5.393 21.352 251.978 -7.268 1.053  -0.001 O3  Q84 19 
Q84 O4  O4  O 0 1 N N N N N N 1.954  22.830 253.741 2.029  -4.168 0.461  O4  Q84 20 
Q84 O5  O5  O 0 1 N N N N N N 3.050  26.648 255.950 4.696  -0.690 -0.204 O5  Q84 21 
Q84 H1  H1  H 0 1 N N N N N N -0.779 31.515 255.237 4.029  4.376  1.631  H1  Q84 22 
Q84 H2  H2  H 0 1 N N N N N N -0.509 30.143 254.109 5.342  3.264  1.174  H2  Q84 23 
Q84 H3  H3  H 0 1 N N N N N N -1.540 29.921 255.563 4.994  4.691  0.169  H3  Q84 24 
Q84 H6  H6  H 0 1 N N N N N N 2.180  28.485 256.026 3.897  1.284  1.107  H6  Q84 25 
Q84 H8  H8  H 0 1 N N N N N N -1.170 25.045 252.032 -1.392 -1.220 0.973  H8  Q84 26 
Q84 H9  H9  H 0 1 N N N N N N -2.261 26.469 251.925 -1.446 -1.512 -0.782 H9  Q84 27 
Q84 H10 H10 H 0 1 N N N N N N -3.494 25.306 253.917 -2.288 1.065  0.620  H10 Q84 28 
Q84 H11 H11 H 0 1 N N N N N N -3.758 24.768 252.224 -2.342 0.773  -1.135 H11 Q84 29 
Q84 H12 H12 H 0 1 N N N N N N -2.209 23.479 254.449 -3.826 -0.895 0.945  H12 Q84 30 
Q84 H13 H13 H 0 1 N N N N N N -4.542 22.835 254.057 -4.834 1.264  -0.964 H13 Q84 31 
Q84 H14 H14 H 0 1 N N N N N N -3.514 21.896 251.348 -6.372 -0.696 -0.640 H14 Q84 32 
Q84 H15 H15 H 0 1 N N N N N N -4.663 23.244 251.643 -6.318 -0.404 1.115  H15 Q84 33 
Q84 H16 H16 H 0 1 N N N N N N -0.934 27.269 253.355 0.058  0.832  -0.315 H16 Q84 34 
Q84 H17 H17 H 0 1 N N N N N N 3.393  24.385 255.022 4.157  -3.052 0.204  H17 Q84 35 
Q84 H18 H18 H 0 1 N N N N N N -1.273 22.099 252.824 -3.976 -0.851 -1.954 H18 Q84 36 
Q84 H19 H19 H 0 1 N N N N N N -2.935 21.313 254.779 -4.684 1.220  1.935  H19 Q84 37 
Q84 H20 H20 H 0 1 N N N N N N -5.716 21.271 251.088 -8.166 0.705  0.084  H20 Q84 38 
Q84 O6  O6  O 0 1 N N N N N N 1.243  31.083 256.603 2.985  3.619  -0.945 O6  Q84 39 
Q84 H4  H4  H 0 1 N N N N N N -0.178 24.020 253.143 0.177  -2.636 0.258  H4  Q84 40 
# 
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 
Q84 O3  C9  SING N N 1  
Q84 C9  C8  SING N N 2  
Q84 O1  C7  SING N N 3  
Q84 C5  C6  SING N N 4  
Q84 C5  N1  SING N N 5  
Q84 C6  C7  SING N N 6  
Q84 C8  C7  SING N N 7  
Q84 C8  O2  SING N N 8  
Q84 N1  C4  SING N N 9  
Q84 N2  C10 SING N N 10 
Q84 N2  C4  SING N N 11 
Q84 O4  C10 DOUB N N 12 
Q84 C10 N3  SING N N 13 
Q84 C4  C3  DOUB N N 14 
Q84 N3  C11 SING N N 15 
Q84 C3  N   SING N N 16 
Q84 C3  C11 SING N N 17 
Q84 N   C2  DOUB N N 18 
Q84 C   C1  SING N N 19 
Q84 C11 O5  DOUB N N 20 
Q84 C2  C1  SING N N 21 
Q84 C   H1  SING N N 22 
Q84 C   H2  SING N N 23 
Q84 C   H3  SING N N 24 
Q84 C2  H6  SING N N 25 
Q84 C5  H8  SING N N 26 
Q84 C5  H9  SING N N 27 
Q84 C6  H10 SING N N 28 
Q84 C6  H11 SING N N 29 
Q84 C7  H12 SING N N 30 
Q84 C8  H13 SING N N 31 
Q84 C9  H14 SING N N 32 
Q84 C9  H15 SING N N 33 
Q84 N1  H16 SING N N 34 
Q84 N3  H17 SING N N 35 
Q84 O1  H18 SING N N 36 
Q84 O2  H19 SING N N 37 
Q84 O3  H20 SING N N 38 
Q84 C1  O6  DOUB N N 39 
Q84 N2  H4  SING N N 40 
# 
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 
Q84 SMILES           ACDLabs              12.01 "CC(=O)/C=N/C=1C(=O)NC(NC=1NCCC(C(O)CO)O)=O"                                                                                                           
Q84 InChI            InChI                1.03  "InChI=1S/C12H18N4O6/c1-6(18)4-14-9-10(15-12(22)16-11(9)21)13-3-2-7(19)8(20)5-17/h4,7-8,17,19-20H,2-3,5H2,1H3,(H3,13,15,16,21,22)/b14-4+/t7-,8+/m0/s1" 
Q84 InChIKey         InChI                1.03  FZDZNUDZZWQFOO-SSOFNSMFSA-N                                                                                                                            
Q84 SMILES_CANONICAL CACTVS               3.385 "CC(=O)C=NC1=C(NCC[C@H](O)[C@H](O)CO)NC(=O)NC1=O"                                                                                                      
Q84 SMILES           CACTVS               3.385 "CC(=O)C=NC1=C(NCC[CH](O)[CH](O)CO)NC(=O)NC1=O"                                                                                                        
Q84 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)/C=N/C1=C(NC(=O)NC1=O)NCC[C@@H]([C@@H](CO)O)O"                                                                                                  
Q84 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C=NC1=C(NC(=O)NC1=O)NCCC(C(CO)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 
Q84 "SYSTEMATIC NAME" ACDLabs              12.01 "1,2-dideoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-erythro-pentitol"      
Q84 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[(~{E})-2-oxidanylidenepropylideneamino]-6-[[(3~{S},4~{R})-3,4,5-tris(oxidanyl)pentyl]amino]-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 
Q84 "Create component" 2019-10-02 RCSB 
Q84 "Initial release"  2020-02-19 RCSB 
Q84 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Q84 
_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      ? 
# 
