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                   2020-02-14
_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
#   #
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.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  44.811  72.565  226.840   1.246   0.919   0.083  C4   Q87   1  
Q87  C5   C2   C  0  1  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  41.722  71.405  228.042  -2.307  -0.217   0.161  C6   Q87   3  
Q87  C8   C4   C  0  1  N  N  R  39.737  72.895  227.499  -4.778  -0.587   0.140  C8   Q87   4  
Q87  N1   N1   N  0  1  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  46.064  74.907  226.166   3.530   2.480  -0.116  N3   Q87   6  
Q87  O6   O1   O  0  1  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  47.388  71.070  224.949   3.455  -1.730  -0.237  C2   Q87   8  
Q87  O2   O2   O  0  1  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  46.311  71.264  225.624   2.616  -1.008   0.464  N    Q87  10  
Q87  C    C6   C  0  1  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  47.799  69.694  224.680   3.653  -3.089   0.081  C1   Q87  12  
Q87  C10  C8   C  0  1  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  46.607  73.771  225.597   3.698   1.163   0.120  C11  Q87  14  
Q87  C3   C10  C  0  1  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  41.262  72.775  227.545  -3.670   0.458  -0.008  C7   Q87  16  
Q87  C9   C12  C  0  1  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  44.381  73.769  227.310   1.187   2.262  -0.159  N2   Q87  18  
Q87  O1   O3   O  0  1  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  39.413  74.206  227.054  -4.619  -1.595  -0.860  O3   Q87  20  
Q87  O4   O5   O  0  1  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  44.520  76.041  227.384   2.194   4.196  -0.465  O5   Q87  22  
Q87  H1   H1   H  0  1  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  43.414  72.324  228.948  -1.321   1.597   0.776  H2   Q87  24  
Q87  H3   H3   H  0  1  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  39.337  72.140  226.806  -4.719  -1.043   1.128  H4   Q87  26  
Q87  H5   H5   H  0  1  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  46.519  75.773  225.959   4.307   3.056  -0.192  H6   Q87  28  
Q87  H7   H7   H  0  1  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  42.759  73.690  228.429  -3.787   1.131   1.898  H8   Q87  30  
Q87  H9   H9   H  0  1  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  47.038  68.885  226.508   4.637  -4.936  -0.334  H10  Q87  32  
Q87  H11  H11  H  0  1  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  41.648  72.918  226.525  -3.730   0.913  -0.997  H15  Q87  34  
Q87  H16  H16  H  0  1  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  39.620  73.354  229.595  -6.236   0.466  -1.047  H17  Q87  36  
Q87  H18  H18  H  0  1  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  38.469  74.304  227.017  -4.661  -1.261  -1.767  H19  Q87  38  
Q87  H20  H20  H  0  1  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  48.936  69.142  224.021   3.045  -3.591   1.006  O7   Q87  40  
Q87  H12  H12  H  0  1  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  
##
