data_UTB
#

_chem_comp.id                                   UTB
_chem_comp.name                                 "1-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-(2-pyren-1-ylethynyl)pyrimidine-2,4-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C27 H20 N2 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-17
_chem_comp.pdbx_modified_date                   2021-07-30
_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                       452.458
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UTB
_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       7NWD
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
UTB  C4      C1   C  0  1  N  N  N  -2.883  10.009   3.251  -2.074  -2.710  -0.046  C4      UTB   1  
UTB  C5      C2   C  0  1  N  N  N  -1.522   9.632   3.629  -1.333  -1.440  -0.067  C5      UTB   2  
UTB  C2      C3   C  0  1  N  N  N  -1.899  11.885   2.021  -4.068  -1.494  -0.125  C2      UTB   3  
UTB  N1      N1   N  0  1  N  N  N  -0.618  11.469   2.422  -3.409  -0.324  -0.150  N1      UTB   4  
UTB  "O5'"   O1   O  0  1  N  N  N  -1.391  15.528   1.195  -7.409   1.792   2.487  "O5'"   UTB   5  
UTB  "C5'"   C4   C  0  1  N  N  N  -0.084  15.801   1.682  -7.545   1.297   1.153  "C5'"   UTB   6  
UTB  "C4'"   C5   C  0  1  N  N  R   0.787  14.537   1.674  -6.297   1.658   0.346  "C4'"   UTB   7  
UTB  "O4'"   O2   O  0  1  N  N  N   0.314  13.642   2.659  -5.142   0.955   0.853  "O4'"   UTB   8  
UTB  "C3'"   C6   C  0  1  N  N  S   0.773  13.760   0.348  -6.422   1.145  -1.111  "C3'"   UTB   9  
UTB  "C2'"   C7   C  0  1  N  N  N   1.133  12.356   0.820  -4.939   1.014  -1.537  "C2'"   UTB  10  
UTB  "O3'"   O3   O  0  1  N  N  N   1.654  14.347  -0.601  -7.106   2.096  -1.930  "O3'"   UTB  11  
UTB  "C1'"   C8   C  0  1  N  N  R   0.582  12.325   2.240  -4.170   0.927  -0.205  "C1'"   UTB  12  
UTB  C6      C9   C  0  1  N  N  N  -0.460  10.358   3.201  -2.045  -0.276  -0.119  C6      UTB  13  
UTB  C7      C10  C  0  1  N  N  N  -1.240   8.460   4.451   0.098  -1.424  -0.032  C7      UTB  14  
UTB  O4      O4   O  0  1  N  N  N  -3.922   9.448   3.600  -1.484  -3.773   0.000  O4      UTB  15  
UTB  N3      N2   N  0  1  N  N  N  -2.961  11.112   2.431  -3.423  -2.672  -0.075  N3      UTB  16  
UTB  O2      O5   O  0  1  N  N  N  -2.131  12.885   1.345  -5.284  -1.487  -0.155  O2      UTB  17  
UTB  C11     C11  C  0  1  N  N  N  -0.959   7.488   5.106   1.272  -1.412  -0.004  C11     UTB  18  
UTB  C12     C12  C  0  1  Y  N  N  -0.573   6.305   5.872   2.704  -1.396   0.030  C12     UTB  19  
UTB  C13     C13  C  0  1  Y  N  N   0.789   6.011   6.121   3.328  -0.242   0.011  C13     UTB  20  
UTB  C14     C14  C  0  1  Y  N  N  -1.582   5.442   6.336   3.428  -2.672   0.093  C14     UTB  21  
UTB  C15     C15  C  0  1  Y  N  N  -1.243   4.268   7.032   4.741  -2.745   0.128  C15     UTB  22  
UTB  C16     C16  C  0  1  Y  N  N   1.125   4.829   6.821   4.801  -0.225   0.046  C16     UTB  23  
UTB  C17     C17  C  0  1  Y  N  N   0.108   3.954   7.263   5.535  -1.503   0.104  C17     UTB  24  
UTB  C18     C18  C  0  1  Y  N  N   1.825   6.870   5.687   2.597   1.035  -0.046  C18     UTB  25  
UTB  C19     C19  C  0  1  Y  N  N   3.172   6.560   5.951   3.256   2.178  -0.065  C19     UTB  26  
UTB  C20     C20  C  0  1  Y  N  N   2.478   4.511   7.073   5.453   0.906   0.028  C20     UTB  27  
UTB  C21     C21  C  0  1  Y  N  N   3.503   5.380   6.639   4.728   2.188  -0.031  C21     UTB  28  
UTB  C22     C22  C  0  1  Y  N  N   4.852   5.054   6.881   5.413   3.307  -0.050  C22     UTB  29  
UTB  C23     C23  C  0  1  Y  N  N   5.181   3.855   7.541   6.881   3.322  -0.016  C23     UTB  30  
UTB  C24     C24  C  0  1  Y  N  N   2.811   3.314   7.747   6.927   0.914   0.063  C24     UTB  31  
UTB  C25     C25  C  0  1  Y  N  N   4.161   2.985   7.970   7.604   2.223   0.036  C25     UTB  32  
UTB  C26     C26  C  0  1  Y  N  N   1.792   2.444   8.174   7.584  -0.220   0.114  C26     UTB  33  
UTB  C27     C27  C  0  1  Y  N  N   0.445   2.765   7.931   6.846  -1.501   0.137  C27     UTB  34  
UTB  "HO5'"  H1   H  0  0  N  N  N  -1.573  14.599   1.279  -8.166   1.599   3.057  "HO5'"  UTB  35  
UTB  "H5'"   H2   H  0  1  N  N  N   0.385  16.564   1.043  -7.661   0.214   1.178  "H5'"   UTB  36  
UTB  "H5''"  H3   H  0  0  N  N  N  -0.157  16.180   2.712  -8.422   1.746   0.687  "H5''"  UTB  37  
UTB  "H4'"   H4   H  0  1  N  N  N   1.824  14.828   1.895  -6.128   2.735   0.363  "H4'"   UTB  38  
UTB  "H3'"   H5   H  0  1  N  N  N  -0.255  13.750  -0.043  -6.922   0.177  -1.141  "H3'"   UTB  39  
UTB  "H2''"  H6   H  0  0  N  N  N   0.652  11.592   0.192  -4.790   0.108  -2.124  "H2''"  UTB  40  
UTB  "H2'"   H7   H  0  1  N  N  N   2.222  12.203   0.814  -4.626   1.891  -2.103  "H2'"   UTB  41  
UTB  H1      H8   H  0  1  N  N  N   1.343  15.215  -0.828  -7.131   1.861  -2.868  H1      UTB  42  
UTB  "H1'"   H9   H  0  1  N  N  N   1.376  11.914   2.881  -3.493   1.776  -0.112  "H1'"   UTB  43  
UTB  H6      H10  H  0  1  N  N  N   0.536  10.050   3.483  -1.533   0.675  -0.135  H6      UTB  44  
UTB  H3      H11  H  0  1  N  N  N  -3.869  11.374   2.105  -3.929  -3.499  -0.058  H3      UTB  45  
UTB  H19     H12  H  0  1  N  N  N  -2.620   5.682   6.157   2.859  -3.590   0.111  H19     UTB  46  
UTB  H20     H13  H  0  1  N  N  N  -2.020   3.608   7.389   5.233  -3.705   0.174  H20     UTB  47  
UTB  H12     H14  H  0  1  N  N  N   1.580   7.773   5.148   1.518   1.036  -0.072  H12     UTB  48  
UTB  H13     H15  H  0  1  N  N  N   3.953   7.230   5.624   2.713   3.111  -0.108  H13     UTB  49  
UTB  H14     H16  H  0  1  N  N  N   5.635   5.725   6.560   4.881   4.246  -0.092  H14     UTB  50  
UTB  H15     H17  H  0  1  N  N  N   6.216   3.603   7.718   7.389   4.274  -0.034  H15     UTB  51  
UTB  H16     H18  H  0  1  N  N  N   4.415   2.063   8.471   8.682   2.280   0.059  H16     UTB  52  
UTB  H17     H19  H  0  1  N  N  N   2.044   1.529   8.689   8.664  -0.219   0.140  H17     UTB  53  
UTB  H18     H20  H  0  1  N  N  N  -0.335   2.094   8.260   7.387  -2.435   0.183  H18     UTB  54  
#   #
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
UTB  "O3'"  "C3'"   SING  N  N   1  
UTB  "C3'"  "C2'"   SING  N  N   2  
UTB  "C3'"  "C4'"   SING  N  N   3  
UTB  "C2'"  "C1'"   SING  N  N   4  
UTB  "O5'"  "C5'"   SING  N  N   5  
UTB  O2     C2      DOUB  N  N   6  
UTB  "C4'"  "C5'"   SING  N  N   7  
UTB  "C4'"  "O4'"   SING  N  N   8  
UTB  C2     N1      SING  N  N   9  
UTB  C2     N3      SING  N  N  10  
UTB  "C1'"  N1      SING  N  N  11  
UTB  "C1'"  "O4'"   SING  N  N  12  
UTB  N1     C6      SING  N  N  13  
UTB  N3     C4      SING  N  N  14  
UTB  C6     C5      DOUB  N  N  15  
UTB  C4     O4      DOUB  N  N  16  
UTB  C4     C5      SING  N  N  17  
UTB  C5     C7      SING  N  N  18  
UTB  C7     C11     TRIP  N  N  19  
UTB  C11    C12     SING  N  N  20  
UTB  C18    C19     DOUB  Y  N  21  
UTB  C18    C13     SING  Y  N  22  
UTB  C12    C13     DOUB  Y  N  23  
UTB  C12    C14     SING  Y  N  24  
UTB  C19    C21     SING  Y  N  25  
UTB  C13    C16     SING  Y  N  26  
UTB  C14    C15     DOUB  Y  N  27  
UTB  C21    C22     DOUB  Y  N  28  
UTB  C21    C20     SING  Y  N  29  
UTB  C16    C20     DOUB  Y  N  30  
UTB  C16    C17     SING  Y  N  31  
UTB  C22    C23     SING  Y  N  32  
UTB  C15    C17     SING  Y  N  33  
UTB  C20    C24     SING  Y  N  34  
UTB  C17    C27     DOUB  Y  N  35  
UTB  C23    C25     DOUB  Y  N  36  
UTB  C24    C25     SING  Y  N  37  
UTB  C24    C26     DOUB  Y  N  38  
UTB  C27    C26     SING  Y  N  39  
UTB  "O5'"  "HO5'"  SING  N  N  40  
UTB  "C5'"  "H5'"   SING  N  N  41  
UTB  "C5'"  "H5''"  SING  N  N  42  
UTB  "C4'"  "H4'"   SING  N  N  43  
UTB  "C3'"  "H3'"   SING  N  N  44  
UTB  "C2'"  "H2''"  SING  N  N  45  
UTB  "C2'"  "H2'"   SING  N  N  46  
UTB  "O3'"  H1      SING  N  N  47  
UTB  "C1'"  "H1'"   SING  N  N  48  
UTB  C6     H6      SING  N  N  49  
UTB  N3     H3      SING  N  N  50  
UTB  C14    H19     SING  N  N  51  
UTB  C15    H20     SING  N  N  52  
UTB  C18    H12     SING  N  N  53  
UTB  C19    H13     SING  N  N  54  
UTB  C22    H14     SING  N  N  55  
UTB  C23    H15     SING  N  N  56  
UTB  C25    H16     SING  N  N  57  
UTB  C26    H17     SING  N  N  58  
UTB  C27    H18     SING  N  N  59  
#   #
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
UTB  InChI             InChI                 1.03   "InChI=1S/C27H20N2O5/c30-14-22-21(31)12-23(34-22)29-13-19(26(32)28-27(29)33)9-5-15-4-6-18-8-7-16-2-1-3-17-10-11-20(15)25(18)24(16)17/h1-4,6-8,10-11,13,21-23,30-31H,12,14H2,(H,28,32,33)/t21-,22+,23+/m0/s1"  
UTB  InChIKey          InChI                 1.03   SBUWMUFDYOCKMX-YTFSRNRJSA-N  
UTB  SMILES_CANONICAL  CACTVS                3.385  "OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C#Cc3ccc4ccc5cccc6ccc3c4c56)C(=O)NC2=O"  
UTB  SMILES            CACTVS                3.385  "OC[CH]1O[CH](C[CH]1O)N2C=C(C#Cc3ccc4ccc5cccc6ccc3c4c56)C(=O)NC2=O"  
UTB  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc2ccc3ccc(c4c3c2c(c1)cc4)C#CC5=CN(C(=O)NC5=O)[C@H]6C[C@@H]([C@H](O6)CO)O"  
UTB  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc2ccc3ccc(c4c3c2c(c1)cc4)C#CC5=CN(C(=O)NC5=O)C6CC(C(O6)CO)O"  
#
_pdbx_chem_comp_identifier.comp_id          UTB
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "1-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-(2-pyren-1-ylethynyl)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
UTB  "Create component"  2021-03-17  PDBE  
UTB  "Initial release"   2021-08-04  RCSB  
##
