data_Q7J
# 
_chem_comp.id                                    Q7J 
_chem_comp.name                                  "1,4-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                     2019-10-01 
_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                     Q7J 
_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        6PUE 
_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 
Q7J C4  C1  C 0 1 N N N N N N 44.577 73.063 227.797 -1.009 -0.881 0.082  C4  Q7J 1  
Q7J C3  C2  C 0 1 N N N N N N 45.756 72.955 227.045 -2.286 -0.314 0.258  C3  Q7J 2  
Q7J C2  C3  C 0 1 N N N N N N 47.194 71.373 226.138 -3.307 1.696  -0.182 C2  Q7J 3  
Q7J N1  N1  N 0 1 N N N N N N 43.880 71.957 228.167 0.109  -0.108 0.161  N1  Q7J 4  
Q7J C6  C4  C 0 1 N N S N N N 41.587 71.838 229.124 2.507  0.368  0.118  C6  Q7J 5  
Q7J C5  C5  C 0 1 N N N N N N 43.087 71.966 229.389 1.431  -0.712 -0.018 C5  Q7J 6  
Q7J C8  C6  C 0 1 N N N N N N 39.469 73.170 228.635 4.965  0.816  0.067  C8  Q7J 7  
Q7J O1  O1  O 0 1 N N N N N N 41.331 70.730 228.258 2.304  1.372  -0.878 O1  Q7J 8  
Q7J N   N2  N 0 1 N N N N N N 46.122 71.633 226.799 -2.434 0.998  0.501  N   Q7J 9  
Q7J C   C7  C 0 1 N N N N N N 46.727 68.968 226.691 -4.396 3.895  -0.785 C   Q7J 10 
Q7J C1  C8  C 0 1 N N N N N N 47.540 69.967 225.918 -3.392 3.091  0.001  C1  Q7J 11 
Q7J C10 C9  C 0 1 N N N N N N 44.791 75.457 227.838 -2.001 -2.998 -0.245 C10 Q7J 12 
Q7J C11 C10 C 0 1 N N N N N N 46.488 74.134 226.638 -3.451 -1.205 0.166  C11 Q7J 13 
Q7J C7  C11 C 0 1 N N R N N N 40.990 73.121 228.544 3.889  -0.263 -0.069 C7  Q7J 14 
Q7J C9  C12 C 0 1 N N N N N N 38.836 74.228 227.759 6.336  0.211  -0.242 C9  Q7J 15 
Q7J N2  N3  N 0 1 N N N N N N 44.139 74.299 228.162 -0.910 -2.221 -0.164 N2  Q7J 16 
Q7J N3  N4  N 0 1 N N N N N N 45.936 75.316 227.097 -3.244 -2.515 -0.081 N3  Q7J 17 
Q7J O2  O2  O 0 1 N N N N N N 41.541 74.255 229.215 4.093  -1.268 0.927  O2  Q7J 18 
Q7J O3  O3  O 0 1 N N N N N N 37.412 74.172 227.818 7.341  1.219  -0.115 O3  Q7J 19 
Q7J O4  O4  O 0 1 N N N N N N 44.374 76.556 228.185 -1.860 -4.185 -0.466 O4  Q7J 20 
Q7J O5  O5  O 0 1 N N N N N N 47.482 74.165 225.916 -4.579 -0.771 0.310  O5  Q7J 21 
Q7J H2  H2  H 0 1 N N N N N N 47.820 72.167 225.757 -3.961 1.203  -0.886 H2  Q7J 22 
Q7J H3  H3  H 0 1 N N N N N N 43.252 71.749 227.418 0.029  0.843  0.336  H3  Q7J 23 
Q7J H4  H4  H 0 1 N N N N N N 41.095 71.652 230.090 2.445  0.820  1.108  H4  Q7J 24 
Q7J H5  H5  H 0 1 N N N N N N 43.405 71.123 230.020 1.587  -1.478 0.742  H5  Q7J 25 
Q7J H6  H6  H 0 1 N N N N N N 43.270 72.912 229.920 1.493  -1.164 -1.008 H6  Q7J 26 
Q7J H7  H7  H 0 1 N N N N N N 39.191 73.374 229.680 4.758  1.625  -0.633 H7  Q7J 27 
Q7J H8  H8  H 0 1 N N N N N N 39.072 72.189 228.335 4.961  1.206  1.085  H8  Q7J 28 
Q7J H9  H9  H 0 1 N N N N N N 41.708 69.942 228.632 2.345  1.040  -1.785 H9  Q7J 29 
Q7J H10 H10 H 0 1 N N N N N N 47.159 67.965 226.563 -5.401 3.538  -0.562 H10 Q7J 30 
Q7J H11 H11 H 0 1 N N N N N N 46.734 69.237 227.758 -4.314 4.946  -0.511 H11 Q7J 31 
Q7J H12 H12 H 0 1 N N N N N N 45.692 68.971 226.319 -4.198 3.781  -1.851 H12 Q7J 32 
Q7J H15 H15 H 0 1 N N N N N N 41.264 73.166 227.480 3.951  -0.715 -1.059 H15 Q7J 33 
Q7J H16 H16 H 0 1 N N N N N N 39.157 74.070 226.719 6.542  -0.598 0.458  H16 Q7J 34 
Q7J H17 H17 H 0 1 N N N N N N 39.169 75.220 228.099 6.339  -0.179 -1.260 H17 Q7J 35 
Q7J H18 H18 H 0 1 N N N N N N 46.424 76.157 226.864 -4.003 -3.116 -0.144 H18 Q7J 36 
Q7J H19 H19 H 0 1 N N N N N N 42.489 74.227 229.160 4.051  -0.936 1.834  H19 Q7J 37 
Q7J H20 H20 H 0 1 N N N N N N 37.045 74.847 227.259 8.237  0.906  -0.298 H20 Q7J 38 
Q7J O6  O6  O 0 1 N N N N N N 48.705 69.838 225.098 -2.656 3.646  0.792  O6  Q7J 39 
Q7J H1  H1  H 0 1 N N N N N N 43.296 74.364 228.695 -0.034 -2.619 -0.283 H1  Q7J 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 
Q7J O5  C11 DOUB N N 1  
Q7J C1  C2  SING N N 2  
Q7J C1  C   SING N N 3  
Q7J C2  N   DOUB N N 4  
Q7J C11 C3  SING N N 5  
Q7J C11 N3  SING N N 6  
Q7J N   C3  SING N N 7  
Q7J C3  C4  DOUB N N 8  
Q7J N3  C10 SING N N 9  
Q7J C9  O3  SING N N 10 
Q7J C9  C8  SING N N 11 
Q7J C4  N2  SING N N 12 
Q7J C4  N1  SING N N 13 
Q7J C10 N2  SING N N 14 
Q7J C10 O4  DOUB N N 15 
Q7J N1  C5  SING N N 16 
Q7J O1  C6  SING N N 17 
Q7J C7  C8  SING N N 18 
Q7J C7  C6  SING N N 19 
Q7J C7  O2  SING N N 20 
Q7J C6  C5  SING N N 21 
Q7J C2  H2  SING N N 22 
Q7J N1  H3  SING N N 23 
Q7J C6  H4  SING N N 24 
Q7J C5  H5  SING N N 25 
Q7J C5  H6  SING N N 26 
Q7J C8  H7  SING N N 27 
Q7J C8  H8  SING N N 28 
Q7J O1  H9  SING N N 29 
Q7J C   H10 SING N N 30 
Q7J C   H11 SING N N 31 
Q7J C   H12 SING N N 32 
Q7J C7  H15 SING N N 33 
Q7J C9  H16 SING N N 34 
Q7J C9  H17 SING N N 35 
Q7J N3  H18 SING N N 36 
Q7J O2  H19 SING N N 37 
Q7J O3  H20 SING N N 38 
Q7J C1  O6  DOUB N N 39 
Q7J N2  H1  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 
Q7J SMILES           ACDLabs              12.01 "C=1(NC(=O)NC(C=1N=[C@H]C(C)=O)=O)NCC(O)C(CCO)O"                                                                                                       
Q7J InChI            InChI                1.03  "InChI=1S/C12H18N4O6/c1-6(18)4-13-9-10(15-12(22)16-11(9)21)14-5-8(20)7(19)2-3-17/h4,7-8,17,19-20H,2-3,5H2,1H3,(H3,14,15,16,21,22)/b13-4+/t7-,8+/m1/s1" 
Q7J InChIKey         InChI                1.03  LFFDRPXUQKVYPE-ZGBHKRMMSA-N                                                                                                                            
Q7J SMILES_CANONICAL CACTVS               3.385 "CC(=O)C=NC1=C(NC[C@H](O)[C@H](O)CCO)NC(=O)NC1=O"                                                                                                      
Q7J SMILES           CACTVS               3.385 "CC(=O)C=NC1=C(NC[CH](O)[CH](O)CCO)NC(=O)NC1=O"                                                                                                        
Q7J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H](CCO)O)O"                                                                                                  
Q7J SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C=NC1=C(NC(=O)NC1=O)NCC(C(CCO)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 
Q7J "SYSTEMATIC NAME" ACDLabs              12.01 "1,4-dideoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-erythro-pentitol"      
Q7J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[(~{E})-2-oxidanylidenepropylideneamino]-6-[[(2~{S},3~{R})-2,3,5-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 
Q7J "Create component" 2019-10-01 RCSB 
Q7J "Initial release"  2020-02-19 RCSB 
Q7J "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Q7J 
_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      ? 
# 
