data_Q87
# 
_chem_comp.id                                    Q87 
_chem_comp.name                                  "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H18 N4 O7" 
_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                        330.294 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Q87 
_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        6PUC 
_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 
Q87 C4  C1  C 0 1 N N N N N N 44.811 72.565 226.840 1.246  0.919  0.083  C4  Q87 1  
Q87 C5  C2  C 0 1 N N N N N N 43.214 71.420 228.354 -1.199 0.828  0.013  C5  Q87 2  
Q87 C6  C3  C 0 1 N N S N N N 41.722 71.405 228.042 -2.307 -0.217 0.161  C6  Q87 3  
Q87 C8  C4  C 0 1 N N R N N N 39.737 72.895 227.499 -4.778 -0.587 0.140  C8  Q87 4  
Q87 N1  N1  N 0 1 N N N N N N 44.154 71.421 227.231 0.105  0.182  0.175  N1  Q87 5  
Q87 N3  N2  N 0 1 N N N N N N 46.064 74.907 226.166 3.530  2.480  -0.116 N3  Q87 6  
Q87 O6  O1  O 0 1 N N N N N N 47.622 73.862 224.906 4.814  0.690  0.240  O6  Q87 7  
Q87 C2  C5  C 0 1 N N N N N N 47.388 71.070 224.949 3.455  -1.730 -0.237 C2  Q87 8  
Q87 O2  O2  O 0 1 N N N N N N 41.813 73.775 228.409 -3.830 1.466  0.992  O2  Q87 9  
Q87 N   N3  N 0 1 N N N N N N 46.311 71.264 225.624 2.616  -1.008 0.464  N   Q87 10 
Q87 C   C6  C 0 1 N N N N N N 47.062 68.625 225.439 4.618  -3.919 -0.725 C   Q87 11 
Q87 C1  C7  C 0 1 N N N N N N 47.799 69.694 224.680 3.653  -3.089 0.081  C1  Q87 12 
Q87 C10 C8  C 0 1 N N N N N N 44.966 74.970 226.985 2.301  3.004  -0.253 C10 Q87 13 
Q87 C11 C9  C 0 1 N N N N N N 46.607 73.771 225.597 3.698  1.163  0.120  C11 Q87 14 
Q87 C3  C10 C 0 1 N N N N N N 45.902 72.553 225.951 2.506  0.309  0.231  C3  Q87 15 
Q87 C7  C11 C 0 1 N N S N N N 41.262 72.775 227.545 -3.670 0.458  -0.008 C7  Q87 16 
Q87 C9  C12 C 0 1 N N N N N N 39.125 72.686 228.875 -6.141 0.087  -0.029 C9  Q87 17 
Q87 N2  N4  N 0 1 N N N N N N 44.381 73.769 227.310 1.187  2.262  -0.159 N2  Q87 18 
Q87 O1  O3  O 0 1 N N N N N N 41.453 70.354 227.111 -2.148 -1.225 -0.839 O1  Q87 19 
Q87 O3  O4  O 0 1 N N N N N N 39.413 74.206 227.054 -4.619 -1.595 -0.860 O3  Q87 20 
Q87 O4  O5  O 0 1 N N N N N N 37.734 72.970 228.856 -7.178 -0.863 0.224  O4  Q87 21 
Q87 O5  O6  O 0 1 N N N N N N 44.520 76.041 227.384 2.194  4.196  -0.465 O5  Q87 22 
Q87 H1  H1  H 0 1 N N N N N N 43.430 70.528 228.960 -1.259 1.283  -0.975 H1  Q87 23 
Q87 H2  H2  H 0 1 N N N N N N 43.414 72.324 228.948 -1.321 1.597  0.776  H2  Q87 24 
Q87 H3  H3  H 0 1 N N N N N N 41.187 71.195 228.980 -2.248 -0.673 1.149  H3  Q87 25 
Q87 H4  H4  H 0 1 N N N N N N 39.337 72.140 226.806 -4.719 -1.043 1.128  H4  Q87 26 
Q87 H5  H5  H 0 1 N N N N N N 43.640 71.105 226.433 0.157  -0.771 0.347  H5  Q87 27 
Q87 H6  H6  H 0 1 N N N N N N 46.519 75.773 225.959 4.307  3.056  -0.192 H6  Q87 28 
Q87 H7  H7  H 0 1 N N N N N N 47.974 71.903 224.590 3.995  -1.283 -1.059 H7  Q87 29 
Q87 H8  H8  H 0 1 N N N N N N 42.759 73.690 228.429 -3.787 1.131  1.898  H8  Q87 30 
Q87 H9  H9  H 0 1 N N N N N N 47.575 67.661 225.308 5.615  -3.485 -0.657 H9  Q87 31 
Q87 H10 H10 H 0 1 N N N N N N 47.038 68.885 226.508 4.637  -4.936 -0.334 H10 Q87 32 
Q87 H11 H11 H 0 1 N N N N N N 46.033 68.547 225.057 4.299  -3.937 -1.767 H11 Q87 33 
Q87 H15 H15 H 0 1 N N N N N N 41.648 72.918 226.525 -3.730 0.913  -0.997 H15 Q87 34 
Q87 H16 H16 H 0 1 N N N N N N 39.276 71.640 229.182 -6.227 0.915  0.675  H16 Q87 35 
Q87 H17 H17 H 0 1 N N N N N N 39.620 73.354 229.595 -6.236 0.466  -1.047 H17 Q87 36 
Q87 H18 H18 H 0 1 N N N N N N 41.758 69.528 227.468 -2.190 -0.891 -1.745 H18 Q87 37 
Q87 H19 H19 H 0 1 N N N N N N 38.469 74.304 227.017 -4.661 -1.261 -1.767 H19 Q87 38 
Q87 H20 H20 H 0 1 N N N N N N 37.371 72.834 229.723 -8.071 -0.504 0.134  H20 Q87 39 
Q87 O7  O7  O 0 1 N N N N N N 48.936 69.142 224.021 3.045  -3.591 1.006  O7  Q87 40 
Q87 H12 H12 H 0 1 N N N N N N 43.594 73.780 227.927 0.322  2.688  -0.266 H12 Q87 41 
# 
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 
Q87 C1  C2  SING N N 1  
Q87 C1  C   SING N N 2  
Q87 O6  C11 DOUB N N 3  
Q87 C2  N   DOUB N N 4  
Q87 C11 C3  SING N N 5  
Q87 C11 N3  SING N N 6  
Q87 N   C3  SING N N 7  
Q87 C3  C4  DOUB N N 8  
Q87 N3  C10 SING N N 9  
Q87 C4  N1  SING N N 10 
Q87 C4  N2  SING N N 11 
Q87 C10 N2  SING N N 12 
Q87 C10 O5  DOUB N N 13 
Q87 O3  C8  SING N N 14 
Q87 O1  C6  SING N N 15 
Q87 N1  C5  SING N N 16 
Q87 C8  C7  SING N N 17 
Q87 C8  C9  SING N N 18 
Q87 C7  C6  SING N N 19 
Q87 C7  O2  SING N N 20 
Q87 C6  C5  SING N N 21 
Q87 O4  C9  SING N N 22 
Q87 C5  H1  SING N N 23 
Q87 C5  H2  SING N N 24 
Q87 C6  H3  SING N N 25 
Q87 C8  H4  SING N N 26 
Q87 N1  H5  SING N N 27 
Q87 N3  H6  SING N N 28 
Q87 C2  H7  SING N N 29 
Q87 O2  H8  SING N N 30 
Q87 C   H9  SING N N 31 
Q87 C   H10 SING N N 32 
Q87 C   H11 SING N N 33 
Q87 C7  H15 SING N N 34 
Q87 C9  H16 SING N N 35 
Q87 C9  H17 SING N N 36 
Q87 O1  H18 SING N N 37 
Q87 O3  H19 SING N N 38 
Q87 O4  H20 SING N N 39 
Q87 C1  O7  DOUB N N 40 
Q87 N2  H12 SING N N 41 
# 
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 
Q87 SMILES           ACDLabs              12.01 "C=1(NCC(C(C(CO)O)O)O)NC(NC(=O)C=1N=[C@H]C(C)=O)=O"                                                                                                          
Q87 InChI            InChI                1.03  "InChI=1S/C12H18N4O7/c1-5(18)2-13-8-10(15-12(23)16-11(8)22)14-3-6(19)9(21)7(20)4-17/h2,6-7,9,17,19-21H,3-4H2,1H3,(H3,14,15,16,22,23)/b13-2+/t6-,7+,9-/m0/s1" 
Q87 InChIKey         InChI                1.03  LXKLTDXEFFOBPT-CEKOQDAHSA-N                                                                                                                                  
Q87 SMILES_CANONICAL CACTVS               3.385 "CC(=O)C=NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O"                                                                                                     
Q87 SMILES           CACTVS               3.385 "CC(=O)C=NC1=C(NC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O"                                                                                                        
Q87 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O"                                                                                                
Q87 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C=NC1=C(NC(=O)NC1=O)NCC(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 
Q87 "SYSTEMATIC NAME" ACDLabs              12.01 "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol"                               
Q87 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[(~{E})-2-oxidanylidenepropylideneamino]-6-[[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(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 
Q87 "Create component" 2019-10-02 RCSB 
Q87 "Initial release"  2020-02-19 RCSB 
Q87 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Q87 
_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      ? 
# 
