data_QBT # _chem_comp.id QBT _chem_comp.name "[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-12-08 _chem_comp.pdbx_modified_date 2022-06-13 _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 324.224 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QBT _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 2Y1J _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 QBT P P P 0 1 N N N -24.442 11.604 -27.837 -4.136 1.144 -0.030 P QBT 1 QBT O1P O1P O 0 1 N N N -24.618 10.594 -28.956 -5.413 0.188 0.191 O1P QBT 2 QBT O2P O2P O 0 1 N N N -24.403 13.061 -28.147 -3.797 1.817 1.244 O2P QBT 3 QBT "O5'" "O5'" O 0 1 N N N -25.520 11.366 -26.668 -2.882 0.260 -0.520 "O5'" QBT 4 QBT "C5'" "C5'" C 0 1 N N N -25.996 10.026 -26.523 -2.268 -0.739 0.297 "C5'" QBT 5 QBT "C4'" "C4'" C 0 1 N N R -27.217 9.991 -25.608 -1.112 -1.385 -0.470 "C4'" QBT 6 QBT "O4'" "O4'" O 0 1 N N N -26.942 10.620 -24.341 -0.053 -0.429 -0.692 "O4'" QBT 7 QBT "C3'" "C3'" C 0 1 N N S -28.372 10.730 -26.249 -0.435 -2.484 0.387 "C3'" QBT 8 QBT "O3'" "O3'" O 0 1 N N N -29.570 9.964 -26.047 -1.105 -3.736 0.234 "O3'" QBT 9 QBT "C2'" "C2'" C 0 1 N N N -28.453 12.029 -25.484 0.987 -2.540 -0.223 "C2'" QBT 10 QBT "C1'" "C1'" C 0 1 N N R -27.940 11.600 -24.077 1.147 -1.182 -0.934 "C1'" QBT 11 QBT N1 N1 N 0 1 N N N -27.330 12.640 -23.249 2.303 -0.467 -0.387 N1 QBT 12 QBT C2 C2 C 0 1 N N N -27.583 12.757 -21.924 2.293 -0.079 0.899 C2 QBT 13 QBT O2 O2 O 0 1 N N N -28.360 12.035 -21.349 1.370 -0.418 1.614 O2 QBT 14 QBT N3 N3 N 0 1 N N N -26.991 13.699 -21.213 3.278 0.676 1.414 N3 QBT 15 QBT C4 C4 C 0 1 N N N -26.078 14.492 -21.738 4.184 1.270 0.616 C4 QBT 16 QBT O4 O4 O 0 1 N N N -25.583 15.372 -21.063 5.112 1.880 1.102 O4 QBT 17 QBT C5 C5 C 0 1 N N S -25.999 14.601 -23.226 4.045 1.177 -0.882 C5 QBT 18 QBT C6 C6 C 0 1 N N N -26.364 13.382 -23.974 3.455 -0.191 -1.247 C6 QBT 19 QBT C5M C5M C 0 1 N N N -24.662 15.200 -23.671 5.421 1.328 -1.534 C5M QBT 20 QBT O3P O3P O 0 1 N Y N -23.055 11.216 -27.163 -4.481 2.251 -1.146 O3P QBT 21 QBT H1P H1P H 0 1 N N N -24.655 11.048 -29.790 -5.691 -0.286 -0.604 H1P QBT 22 QBT "H5'1" "H5'1" H 0 0 N N N -26.275 9.633 -27.512 -1.887 -0.280 1.209 "H5'1" QBT 23 QBT "H5'2" "H5'2" H 0 0 N N N -25.200 9.410 -26.080 -3.004 -1.501 0.554 "H5'2" QBT 24 QBT "H4'" "H4'" H 0 1 N N N -27.471 8.933 -25.447 -1.464 -1.795 -1.417 "H4'" QBT 25 QBT "H3'" "H3'" H 0 1 N N N -28.246 10.893 -27.330 -0.397 -2.190 1.436 "H3'" QBT 26 QBT "H1'" "H1'" H 0 1 N N N -28.815 11.270 -23.498 1.278 -1.338 -2.005 "H1'" QBT 27 QBT HA HA H 0 1 N N N -29.686 9.795 -25.119 -0.718 -4.456 0.751 HA QBT 28 QBT "H2'1" "H2'1" H 0 0 N N N -27.826 12.814 -25.932 1.735 -2.651 0.562 "H2'1" QBT 29 QBT "H2'2" "H2'2" H 0 0 N N N -29.459 12.475 -25.472 1.062 -3.358 -0.941 "H2'2" QBT 30 QBT H61C H61C H 0 0 N N N -25.466 12.764 -24.122 4.208 -0.965 -1.104 H61C QBT 31 QBT H62C H62C H 0 0 N N N -26.785 13.669 -24.949 3.135 -0.182 -2.289 H62C QBT 32 QBT H3 H3 H 0 1 N N N -27.242 13.814 -20.252 3.336 0.794 2.375 H3 QBT 33 QBT H52 H52 H 0 1 N N N -24.669 15.344 -24.762 6.079 0.534 -1.181 H52 QBT 34 QBT H53 H53 H 0 1 N N N -24.512 16.170 -23.175 5.319 1.260 -2.617 H53 QBT 35 QBT H54 H54 H 0 1 N N N -23.845 14.517 -23.397 5.845 2.296 -1.269 H54 QBT 36 QBT H3P H3P H 0 1 N N N -22.387 11.139 -27.834 -5.228 2.821 -0.918 H3P QBT 37 QBT H5M H5M H 0 1 N N N -26.796 15.307 -23.502 3.385 1.969 -1.237 H5M QBT 38 # 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 QBT P O1P SING N N 1 QBT P O2P DOUB N N 2 QBT P "O5'" SING N N 3 QBT P O3P SING N N 4 QBT "O5'" "C5'" SING N N 5 QBT "C5'" "C4'" SING N N 6 QBT "C4'" "O4'" SING N N 7 QBT "C4'" "C3'" SING N N 8 QBT "O4'" "C1'" SING N N 9 QBT "C3'" "O3'" SING N N 10 QBT "C3'" "C2'" SING N N 11 QBT "C2'" "C1'" SING N N 12 QBT "C1'" N1 SING N N 13 QBT N1 C2 SING N N 14 QBT N1 C6 SING N N 15 QBT C2 O2 DOUB N N 16 QBT C2 N3 SING N N 17 QBT N3 C4 SING N N 18 QBT C4 O4 DOUB N N 19 QBT C4 C5 SING N N 20 QBT C5 C5M SING N N 21 QBT O1P H1P SING N N 22 QBT "C5'" "H5'1" SING N N 23 QBT "C5'" "H5'2" SING N N 24 QBT "C4'" "H4'" SING N N 25 QBT "C3'" "H3'" SING N N 26 QBT "C1'" "H1'" SING N N 27 QBT "O3'" HA SING N N 28 QBT "C2'" "H2'1" SING N N 29 QBT "C2'" "H2'2" SING N N 30 QBT C6 H61C SING N N 31 QBT C6 H62C SING N N 32 QBT N3 H3 SING N N 33 QBT C5 C6 SING N N 34 QBT C5 H5M SING N N 35 QBT C5M H52 SING N N 36 QBT C5M H53 SING N N 37 QBT C5M H54 SING N N 38 QBT O3P H3P SING N N 39 # 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 QBT SMILES_CANONICAL CACTVS 3.352 "C[C@H]1CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" QBT SMILES CACTVS 3.352 "C[CH]1CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" QBT SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C[C@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" QBT SMILES "OpenEye OEToolkits" 1.6.1 "CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" QBT InChI InChI 1.03 "InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6-,7+,8+/m0/s1" QBT InChIKey InChI 1.03 PGRQANKWVMVANW-RULNZFCNSA-N # _pdbx_chem_comp_identifier.comp_id QBT _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.6.1 _pdbx_chem_comp_identifier.identifier "[(2R,3S,5R)-3-hydroxy-5-[(5S)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]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 QBT "Create component" 2010-12-08 EBI QBT "Modify descriptor" 2011-06-04 RCSB QBT "Modify one letter code" 2019-05-03 EBI QBT "Modify parent residue" 2022-06-13 RCSB #