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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 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 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 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 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 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 N N N -27.217 9.991 -25.608 -1.112 -1.385 -0.470 "C4'" QBT 6 QBT "O4'" "O4'" O 0 1 N N N 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 N N N -28.372 10.730 -26.249 -0.435 -2.484 0.387 "C3'" QBT 8 QBT "O3'" "O3'" O 0 1 N N N 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 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 N N N -27.940 11.600 -24.077 1.147 -1.182 -0.934 "C1'" QBT 11 QBT N1 N1 N 0 1 N N N 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 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 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 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 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 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 N N N -25.999 14.601 -23.226 4.045 1.177 -0.882 C5 QBT 18 QBT C6 C6 C 0 1 N N N 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 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 N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 # loop_ _software.name _software.version _software.description rdkit 2023.03.3 'Core functionality.' pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal QBT P P 9.603 -4.683 1 QBT O1P O 10.485 -5.896 2 QBT O2P O 10.817 -3.801 3 QBT "O5'" O 8.722 -3.469 4 QBT "C5'" C 7.230 -3.626 5 QBT "C4'" C 6.348 -2.412 6 QBT "O4'" O 6.812 -0.986 7 QBT "C3'" C 4.848 -2.412 8 QBT "O3'" O 3.966 -3.626 9 QBT "C2'" C 4.385 -0.986 10 QBT "C1'" C 5.598 -0.104 11 QBT N1 N 5.598 1.396 12 QBT C2 C 6.897 2.146 13 QBT O2 O 8.196 1.396 14 QBT N3 N 6.897 3.646 15 QBT C4 C 5.598 4.396 16 QBT O4 O 5.598 5.896 17 QBT C5 C 4.299 3.646 18 QBT C6 C 4.299 2.146 19 QBT C5M C 3.000 4.396 20 QBT O3P O 8.390 -5.564 21 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal QBT P O1P SINGLE NONE 1 QBT P O2P DOUBLE NONE 2 QBT P "O5'" SINGLE NONE 3 QBT P O3P SINGLE NONE 4 QBT "O5'" "C5'" SINGLE NONE 5 QBT "C4'" "C5'" SINGLE BEGINDASH 6 QBT "C4'" "O4'" SINGLE NONE 7 QBT "C4'" "C3'" SINGLE NONE 8 QBT "O4'" "C1'" SINGLE NONE 9 QBT "C3'" "O3'" SINGLE BEGINWEDGE 10 QBT "C3'" "C2'" SINGLE NONE 11 QBT "C2'" "C1'" SINGLE NONE 12 QBT "C1'" N1 SINGLE BEGINDASH 13 QBT N1 C2 SINGLE NONE 14 QBT N1 C6 SINGLE NONE 15 QBT C2 O2 DOUBLE NONE 16 QBT C2 N3 SINGLE NONE 17 QBT N3 C4 SINGLE NONE 18 QBT C4 O4 DOUBLE NONE 19 QBT C4 C5 SINGLE NONE 20 QBT C5 C5M SINGLE BEGINDASH 21 QBT C5 C6 SINGLE NONE 22 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys QBT MurckoScaffold S1 scaffold 'O=C1CCN([C@H]2CCCO2)C(=O)N1' InChI=1S/C8H12N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h7H,1-5H2,(H,9,11,12)/t7-/m1/s1 ZAERJFADDUTCMT-SSDOTTSWSA-N QBT amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N QBT deoxyribose F2 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N QBT phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal QBT "C4'" S1 1 QBT "O4'" S1 1 QBT "C3'" S1 1 QBT "C2'" S1 1 QBT "C1'" S1 1 QBT N1 S1 1 QBT C2 S1 1 QBT O2 S1 1 QBT N3 S1 1 QBT C4 S1 1 QBT O4 S1 1 QBT C5 S1 1 QBT C6 S1 1 QBT N3 F1 1 QBT C4 F1 1 QBT O4 F1 1 QBT C5 F1 1 QBT "C1'" F2 1 QBT "C2'" F2 1 QBT "C3'" F2 1 QBT "O3'" F2 1 QBT "C4'" F2 1 QBT "O4'" F2 1 QBT "C5'" F2 1 QBT "O5'" F2 1 QBT O1P F3 1 QBT P F3 1 QBT O2P F3 1 QBT "O5'" F3 1 QBT O3P F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id QBT _pdbe_chem_comp_rdkit_properties.exactmw 324.072 _pdbe_chem_comp_rdkit_properties.amw 324.226 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 10 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 4 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8 _pdbe_chem_comp_rdkit_properties.NumHBD 4 _pdbe_chem_comp_rdkit_properties.NumHBA 8 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 38 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 3 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 144.007 _pdbe_chem_comp_rdkit_properties.tpsa 145.630 _pdbe_chem_comp_rdkit_properties.CrippenClogP -1.240 _pdbe_chem_comp_rdkit_properties.CrippenMR 66.690 _pdbe_chem_comp_rdkit_properties.chi0v 10.502 _pdbe_chem_comp_rdkit_properties.chi1v 6.284 _pdbe_chem_comp_rdkit_properties.chi2v 2.220 _pdbe_chem_comp_rdkit_properties.chi3v 2.220 _pdbe_chem_comp_rdkit_properties.chi4v 1.321 _pdbe_chem_comp_rdkit_properties.chi0n 26.608 _pdbe_chem_comp_rdkit_properties.chi1n 12.995 _pdbe_chem_comp_rdkit_properties.chi2n 1.905 _pdbe_chem_comp_rdkit_properties.chi3n 1.905 _pdbe_chem_comp_rdkit_properties.chi4n 1.126 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.030 _pdbe_chem_comp_rdkit_properties.kappa1 4.985 _pdbe_chem_comp_rdkit_properties.kappa2 5.993 _pdbe_chem_comp_rdkit_properties.kappa3 3.997 _pdbe_chem_comp_rdkit_properties.Phi 1.423 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id QBT UniChem PDBe QBT QBT UniChem PubChem 42628620 # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal QBT P 4.025 2.186 0.535 ETKDGv3 1 QBT O1P 2.866 3.340 0.097 ETKDGv3 2 QBT O2P 5.374 2.616 0.007 ETKDGv3 3 QBT "O5'" 3.624 0.670 -0.133 ETKDGv3 4 QBT "C5'" 2.381 0.270 0.395 ETKDGv3 5 QBT "C4'" 1.961 -1.061 -0.240 ETKDGv3 6 QBT "O4'" 0.799 -1.533 0.411 ETKDGv3 7 QBT "C3'" 1.678 -0.915 -1.745 ETKDGv3 8 QBT "O3'" 2.307 -1.932 -2.489 ETKDGv3 9 QBT "C2'" 0.179 -1.018 -1.833 ETKDGv3 10 QBT "C1'" -0.182 -1.781 -0.572 ETKDGv3 11 QBT N1 -1.514 -1.383 -0.087 ETKDGv3 12 QBT C2 -2.692 -2.095 -0.506 ETKDGv3 13 QBT O2 -2.607 -3.255 -0.992 ETKDGv3 14 QBT N3 -3.973 -1.474 -0.381 ETKDGv3 15 QBT C4 -4.068 -0.092 -0.024 ETKDGv3 16 QBT O4 -5.202 0.456 0.038 ETKDGv3 17 QBT C5 -2.807 0.718 0.179 ETKDGv3 18 QBT C6 -1.692 -0.181 0.743 ETKDGv3 19 QBT C5M -3.042 1.918 1.107 ETKDGv3 20 QBT O3P 4.100 2.079 2.223 ETKDGv3 21 QBT H1P 2.804 3.273 -0.889 ETKDGv3 22 QBT "H5'1" 1.590 1.027 0.188 ETKDGv3 23 QBT "H5'2" 2.462 0.116 1.495 ETKDGv3 24 QBT "H4'" 2.780 -1.796 -0.071 ETKDGv3 25 QBT "H3'" 2.014 0.066 -2.148 ETKDGv3 26 QBT "H1'" -0.165 -2.872 -0.789 ETKDGv3 27 QBT HA 1.997 -2.809 -2.140 ETKDGv3 28 QBT "H2'1" -0.159 -1.552 -2.749 ETKDGv3 29 QBT "H2'2" -0.264 0.002 -1.816 ETKDGv3 30 QBT H61C -1.953 -0.500 1.776 ETKDGv3 31 QBT H62C -0.749 0.404 0.798 ETKDGv3 32 QBT H3 -4.839 -2.015 -0.603 ETKDGv3 33 QBT H52 -3.411 1.580 2.099 ETKDGv3 34 QBT H53 -2.096 2.483 1.248 ETKDGv3 35 QBT H54 -3.789 2.609 0.660 ETKDGv3 36 QBT H3P 4.746 1.350 2.402 ETKDGv3 37 QBT H5M -2.483 1.102 -0.812 ETKDGv3 38 #