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 ##