data_QGJ # _chem_comp.id QGJ _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-2,4-dioxo-N-(3-phenylpropyl)-1,2,3,4-tetrahydropyrimidine-5-carboxamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H24 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-10-28 _chem_comp.pdbx_modified_date 2021-10-29 _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 469.382 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QGJ _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 6USL _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 QGJ "C1'" C1 C 0 1 N N R 22.604 -29.791 -39.458 2.456 1.552 -0.885 "C1'" QGJ 1 QGJ C2 C2 C 0 1 N N N 20.984 -28.022 -38.880 1.174 0.899 1.065 C2 QGJ 2 QGJ "C2'" C3 C 0 1 N N N 22.594 -31.105 -40.231 3.024 2.848 -0.274 "C2'" QGJ 3 QGJ "C3'" C4 C 0 1 N N R 23.704 -31.617 -39.419 4.412 2.433 0.272 "C3'" QGJ 4 QGJ C4 C5 C 0 1 N N N 20.160 -26.505 -40.650 -1.139 0.561 1.060 C4 QGJ 5 QGJ "C4'" C6 C 0 1 N N R 24.717 -30.509 -39.403 4.710 1.148 -0.541 "C4'" QGJ 6 QGJ C5 C7 C 0 1 N N N 21.058 -27.245 -41.634 -1.156 0.908 -0.370 C5 QGJ 7 QGJ "C5'" C8 C 0 1 N N N 25.820 -30.485 -40.439 5.695 0.251 0.211 "C5'" QGJ 8 QGJ C6 C9 C 0 1 N N N 21.806 -28.276 -41.239 0.043 1.226 -0.976 C6 QGJ 9 QGJ CAP C10 C 0 1 N N N 21.233 -27.018 -43.127 -2.414 0.910 -1.133 CAP QGJ 10 QGJ CAR C11 C 0 1 N N N 19.801 -25.015 -43.872 -4.783 0.384 -1.344 CAR QGJ 11 QGJ CAT C12 C 0 1 N N N 19.186 -24.850 -45.282 -5.923 -0.115 -0.453 CAT QGJ 12 QGJ CAU C13 C 0 1 N N N 17.837 -25.621 -45.201 -7.206 -0.224 -1.279 CAU QGJ 13 QGJ CAV C14 C 0 1 Y N N 17.732 -26.726 -46.261 -8.328 -0.715 -0.401 CAV QGJ 14 QGJ CAW C15 C 0 1 Y N N 17.722 -26.375 -47.609 -8.563 -2.071 -0.273 CAW QGJ 15 QGJ CAX C16 C 0 1 Y N N 17.609 -27.359 -48.579 -9.589 -2.522 0.536 CAX QGJ 16 QGJ CAY C17 C 0 1 Y N N 17.491 -28.695 -48.179 -10.380 -1.616 1.218 CAY QGJ 17 QGJ CAZ C18 C 0 1 Y N N 17.472 -29.040 -46.818 -10.145 -0.260 1.091 CAZ QGJ 18 QGJ CBA C19 C 0 1 Y N N 17.598 -28.049 -45.846 -9.119 0.191 0.281 CBA QGJ 19 QGJ N1 N1 N 0 1 N N N 21.792 -28.738 -39.860 1.185 1.214 -0.240 N1 QGJ 20 QGJ N3 N2 N 0 1 N N N 20.157 -26.916 -39.296 0.042 0.575 1.712 N3 QGJ 21 QGJ NAQ N3 N 0 1 N N N 20.709 -26.086 -44.097 -3.555 0.488 -0.553 NAQ QGJ 22 QGJ O2 O1 O 0 1 N N N 21.000 -28.421 -37.758 2.223 0.902 1.679 O2 QGJ 23 QGJ "O3'" O2 O 0 1 N N N 24.250 -32.978 -39.652 4.346 2.148 1.670 "O3'" QGJ 24 QGJ O4 O3 O 0 1 N N N 19.505 -25.587 -40.990 -2.168 0.268 1.641 O4 QGJ 25 QGJ "O4'" O4 O 0 1 N N N 24.004 -29.216 -39.471 3.419 0.511 -0.650 "O4'" QGJ 26 QGJ "O5'" O5 O 0 1 N N N 25.360 -29.999 -41.637 6.042 -0.868 -0.609 "O5'" QGJ 27 QGJ OAS O6 O 0 1 N N N 21.971 -27.761 -43.617 -2.424 1.292 -2.288 OAS QGJ 28 QGJ OP1 O7 O 0 1 N N N 25.641 -29.976 -44.165 6.597 -2.590 1.151 OP1 QGJ 29 QGJ OP2 O8 O 0 1 N N N 26.783 -31.786 -42.954 7.116 -3.181 -1.248 OP2 QGJ 30 QGJ P P1 P 0 1 N N N 26.274 -30.400 -42.970 7.061 -2.020 -0.134 P QGJ 31 QGJ O1 O9 O 0 1 N Y N 27.463 -29.454 -42.971 8.531 -1.391 0.058 O1 QGJ 32 QGJ H1 H1 H 0 1 N N N 22.367 -30.035 -38.412 2.305 1.683 -1.956 H1 QGJ 33 QGJ H2 H2 H 0 1 N N N 21.661 -31.678 -40.123 3.129 3.616 -1.040 H2 QGJ 34 QGJ H3 H3 H 0 1 N N N 22.836 -30.996 -41.298 2.385 3.200 0.536 H3 QGJ 35 QGJ H4 H4 H 0 1 N N N 23.312 -31.646 -38.392 5.156 3.203 0.068 H4 QGJ 36 QGJ H5 H5 H 0 1 N N N 25.212 -30.550 -38.421 5.098 1.399 -1.528 H5 QGJ 37 QGJ H6 H6 H 0 1 N N N 26.197 -31.508 -40.587 6.594 0.819 0.449 H6 QGJ 38 QGJ H7 H7 H 0 1 N N N 26.637 -29.842 -40.080 5.234 -0.103 1.132 H7 QGJ 39 QGJ H8 H8 H 0 1 N N N 22.436 -28.779 -41.958 0.073 1.487 -2.024 H8 QGJ 40 QGJ H9 H9 H 0 1 N N N 20.324 -24.103 -43.550 -4.629 -0.319 -2.164 H9 QGJ 41 QGJ H10 H10 H 0 1 N N N 19.037 -25.282 -43.127 -5.040 1.363 -1.748 H10 QGJ 42 QGJ H11 H11 H 0 1 N N N 19.842 -25.290 -46.048 -5.666 -1.094 -0.049 H11 QGJ 43 QGJ H12 H12 H 0 1 N N N 19.015 -23.788 -45.512 -6.077 0.587 0.366 H12 QGJ 44 QGJ H13 H13 H 0 1 N N N 17.013 -24.908 -45.351 -7.462 0.755 -1.683 H13 QGJ 45 QGJ H14 H14 H 0 1 N N N 17.750 -26.078 -44.204 -7.052 -0.926 -2.098 H14 QGJ 46 QGJ H15 H15 H 0 1 N N N 17.802 -25.338 -47.898 -7.945 -2.779 -0.806 H15 QGJ 47 QGJ H16 H16 H 0 1 N N N 17.612 -27.099 -49.627 -9.773 -3.581 0.635 H16 QGJ 48 QGJ H17 H17 H 0 1 N N N 17.414 -29.470 -48.927 -11.182 -1.968 1.849 H17 QGJ 49 QGJ H18 H18 H 0 1 N N N 17.360 -30.073 -46.524 -10.762 0.448 1.623 H18 QGJ 50 QGJ H19 H19 H 0 1 N N N 17.592 -28.301 -44.796 -8.933 1.250 0.184 H19 QGJ 51 QGJ H20 H20 H 0 1 N N N 19.583 -26.441 -38.629 0.074 0.349 2.655 H20 QGJ 52 QGJ H21 H21 H 0 1 N N N 21.022 -26.208 -45.039 -3.562 0.254 0.388 H21 QGJ 53 QGJ H22 H22 H 0 1 N N N 24.959 -33.144 -39.042 4.074 2.901 2.213 H22 QGJ 54 QGJ H23 H23 H 0 1 N N N 26.599 -32.201 -43.788 7.712 -3.910 -1.028 H23 QGJ 55 QGJ H24 H24 H 0 1 N N N 27.421 -28.893 -43.737 8.899 -0.998 -0.745 H24 QGJ 56 # # 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 QGJ CAX CAY DOUB Y N 1 QGJ CAX CAW SING Y N 2 QGJ CAY CAZ SING Y N 3 QGJ CAW CAV DOUB Y N 4 QGJ CAZ CBA DOUB Y N 5 QGJ CAV CBA SING Y N 6 QGJ CAV CAU SING N N 7 QGJ CAT CAU SING N N 8 QGJ CAT CAR SING N N 9 QGJ OP1 P DOUB N N 10 QGJ NAQ CAR SING N N 11 QGJ NAQ CAP SING N N 12 QGJ OAS CAP DOUB N N 13 QGJ CAP C5 SING N N 14 QGJ P OP2 SING N N 15 QGJ P "O5'" SING N N 16 QGJ "O5'" "C5'" SING N N 17 QGJ C5 C6 DOUB N N 18 QGJ C5 C4 SING N N 19 QGJ C6 N1 SING N N 20 QGJ O4 C4 DOUB N N 21 QGJ C4 N3 SING N N 22 QGJ "C5'" "C4'" SING N N 23 QGJ "C2'" "C1'" SING N N 24 QGJ "C2'" "C3'" SING N N 25 QGJ N1 "C1'" SING N N 26 QGJ N1 C2 SING N N 27 QGJ "O3'" "C3'" SING N N 28 QGJ "O4'" "C1'" SING N N 29 QGJ "O4'" "C4'" SING N N 30 QGJ "C3'" "C4'" SING N N 31 QGJ N3 C2 SING N N 32 QGJ C2 O2 DOUB N N 33 QGJ P O1 SING N N 34 QGJ "C1'" H1 SING N N 35 QGJ "C2'" H2 SING N N 36 QGJ "C2'" H3 SING N N 37 QGJ "C3'" H4 SING N N 38 QGJ "C4'" H5 SING N N 39 QGJ "C5'" H6 SING N N 40 QGJ "C5'" H7 SING N N 41 QGJ C6 H8 SING N N 42 QGJ CAR H9 SING N N 43 QGJ CAR H10 SING N N 44 QGJ CAT H11 SING N N 45 QGJ CAT H12 SING N N 46 QGJ CAU H13 SING N N 47 QGJ CAU H14 SING N N 48 QGJ CAW H15 SING N N 49 QGJ CAX H16 SING N N 50 QGJ CAY H17 SING N N 51 QGJ CAZ H18 SING N N 52 QGJ CBA H19 SING N N 53 QGJ N3 H20 SING N N 54 QGJ NAQ H21 SING N N 55 QGJ "O3'" H22 SING N N 56 QGJ OP2 H23 SING N N 57 QGJ O1 H24 SING N N 58 # # 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 QGJ SMILES ACDLabs 12.01 "C1(CC(C(COP(=O)(O)O)O1)O)N2C(=O)NC(C(=C2)C(NCCCc3ccccc3)=O)=O" QGJ InChI InChI 1.03 "InChI=1S/C19H24N3O9P/c23-14-9-16(31-15(14)11-30-32(27,28)29)22-10-13(18(25)21-19(22)26)17(24)20-8-4-7-12-5-2-1-3-6-12/h1-3,5-6,10,14-16,23H,4,7-9,11H2,(H,20,24)(H,21,25,26)(H2,27,28,29)/t14-,15-,16-/m1/s1" QGJ InChIKey InChI 1.03 HDAALGCFEARBOF-BZUAXINKSA-N QGJ SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCCCc3ccccc3)C(=O)NC2=O" QGJ SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCCCc3ccccc3)C(=O)NC2=O" QGJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CCCNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@H]([C@H](O3)COP(=O)(O)O)O" QGJ SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CCCNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(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 QGJ "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-2,4-dioxo-N-(3-phenylpropyl)-1,2,3,4-tetrahydropyrimidine-5-carboxamide" QGJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},5~{R})-5-[2,4-bis(oxidanylidene)-5-(3-phenylpropylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site QGJ "Create component" 2019-10-28 RCSB QGJ "Initial release" 2021-11-03 RCSB ##