data_F6X # _chem_comp.id F6X _chem_comp.name "[(2R,3R)-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-04-03 _chem_comp.pdbx_modified_date 2020-11-20 _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 336.238 _chem_comp.one_letter_code ? _chem_comp.three_letter_code F6X _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 7BPF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 F6X "C1'" C1 C 0 1 N N N N N N -25.542 -29.541 16.976 -1.249 2.899 -0.353 "C1'" F6X 1 F6X N1 N1 N 0 1 N N N N N N -22.849 -24.581 15.626 2.877 -0.544 0.438 N1 F6X 2 F6X C6 C2 C 0 1 N N N N N N -23.354 -23.868 14.535 3.229 -1.557 -0.402 C6 F6X 3 F6X C5 C3 C 0 1 N N N N N N -23.394 -22.484 14.521 4.503 -1.630 -0.854 C5 F6X 4 F6X C4 C4 C 0 1 N N N N N N -22.921 -21.814 15.639 5.431 -0.652 -0.441 C4 F6X 5 F6X N3 N2 N 0 1 N N N N N N -22.437 -22.561 16.733 5.043 0.316 0.379 N3 F6X 6 F6X C2 C5 C 0 1 N N N N N N -22.401 -23.941 16.714 3.786 0.374 0.815 C2 F6X 7 F6X O2 O1 O 0 1 N N N N N N -21.969 -24.558 17.689 3.453 1.274 1.568 O2 F6X 8 F6X N4 N3 N 0 1 N N N N N N -22.936 -20.495 15.658 6.732 -0.702 -0.885 N4 F6X 9 F6X "C2'" C6 C 0 1 N N R N N N -25.718 -28.439 15.948 -1.418 1.418 -0.697 "C2'" F6X 10 F6X "C3'" C7 C 0 1 N N R N N N -26.338 -28.992 14.677 -2.894 1.032 -0.576 "C3'" F6X 11 F6X "O3'" O2 O 0 1 N N N N N N -25.343 -29.766 14.048 -3.041 -0.368 -0.825 "O3'" F6X 12 F6X OP1 O3 O 0 1 N N N N N N -27.249 -30.837 12.395 -5.143 -0.856 0.485 OP1 F6X 13 F6X P P1 P 0 1 N N N N N N -25.687 -30.738 12.860 -3.784 -1.366 0.197 P F6X 14 F6X OP2 O4 O 0 1 N N N N N N -24.616 -31.881 12.370 -3.889 -2.830 -0.465 OP2 F6X 15 F6X C3A C8 C 0 1 N N N N N N -26.766 -27.829 13.765 -3.713 1.821 -1.599 C3A F6X 16 F6X "O1'" O5 O 0 1 N N N N N N -26.730 -29.532 17.789 -1.815 3.157 0.934 "O1'" F6X 17 F6X "N2'" N4 N 0 1 N N N N N N -24.432 -27.810 15.599 -0.623 0.608 0.228 "N2'" F6X 18 F6X C2A C9 C 0 1 N N N N N N -24.143 -26.584 16.041 0.682 0.384 -0.022 C2A F6X 19 F6X O2A O6 O 0 1 N N N N N N -24.866 -25.912 16.771 1.199 0.854 -1.014 O2A F6X 20 F6X C2B C10 C 0 1 N N N N N N -22.819 -26.050 15.564 1.500 -0.450 0.930 C2B F6X 21 F6X H1 H1 H 0 1 N N N N N N -25.431 -30.514 16.475 -0.188 3.151 -0.340 H1 F6X 22 F6X H2 H2 H 0 1 N N N N N N -24.655 -29.345 17.596 -1.757 3.507 -1.101 H2 F6X 23 F6X H3 H3 H 0 1 N N N N N N -23.724 -24.412 13.678 2.499 -2.294 -0.704 H3 F6X 24 F6X H4 H4 H 0 1 N N N N N N -23.780 -21.945 13.669 4.804 -2.424 -1.521 H4 F6X 25 F6X H5 H5 H 0 1 N N N N N N -22.599 -20.003 16.461 7.014 -1.412 -1.484 H5 F6X 26 F6X H6 H6 H 0 1 N N N N N N -23.284 -19.988 14.870 7.369 -0.029 -0.599 H6 F6X 27 F6X H7 H7 H 0 1 N N N N N N -26.392 -27.676 16.364 -1.079 1.242 -1.718 H7 F6X 28 F6X H8 H8 H 0 1 N N N N N N -27.218 -29.602 14.929 -3.248 1.262 0.429 H8 F6X 29 F6X HOP2 H10 H 0 0 N N N N N N -25.062 -32.522 11.828 -4.327 -3.485 0.096 H10 F6X 30 F6X H11 H11 H 0 1 N N N N N N -27.542 -27.234 14.268 -4.764 1.546 -1.513 H11 F6X 31 F6X H12 H12 H 0 1 N N N N N N -25.896 -27.191 13.552 -3.601 2.888 -1.409 H12 F6X 32 F6X H13 H13 H 0 1 N N N N N N -27.166 -28.231 12.822 -3.359 1.591 -2.604 H13 F6X 33 F6X H14 H14 H 0 1 N Y N N N N -26.666 -30.210 18.452 -1.677 4.060 1.251 H14 F6X 34 F6X H15 H15 H 0 1 N N N N N N -23.774 -28.303 15.030 -1.036 0.232 1.021 H15 F6X 35 F6X H16 H16 H 0 1 N N N N N N -22.642 -26.373 14.527 1.070 -1.449 0.999 H16 F6X 36 F6X H17 H17 H 0 1 N N N N N N -22.013 -26.431 16.209 1.497 0.015 1.916 H17 F6X 37 F6X OP3 OP4 O 0 1 N Y N N N N -25.485 -29.782 11.743 -2.943 -1.456 1.566 OP4 F6X 38 F6X HOP3 H9 H 0 0 N Y N N N N -26.305 -29.658 11.279 -2.027 -1.742 1.447 H9 F6X 39 # 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 F6X OP2 P SING N N 1 F6X OP1 P DOUB N N 2 F6X P "O3'" SING N N 3 F6X C3A "C3'" SING N N 4 F6X "O3'" "C3'" SING N N 5 F6X C5 C6 DOUB N N 6 F6X C5 C4 SING N N 7 F6X C6 N1 SING N N 8 F6X "C3'" "C2'" SING N N 9 F6X C2B N1 SING N N 10 F6X C2B C2A SING N N 11 F6X "N2'" "C2'" SING N N 12 F6X "N2'" C2A SING N N 13 F6X N1 C2 SING N N 14 F6X C4 N4 SING N N 15 F6X C4 N3 DOUB N N 16 F6X "C2'" "C1'" SING N N 17 F6X C2A O2A DOUB N N 18 F6X C2 N3 SING N N 19 F6X C2 O2 DOUB N N 20 F6X "C1'" "O1'" SING N N 21 F6X "C1'" H1 SING N N 22 F6X "C1'" H2 SING N N 23 F6X C6 H3 SING N N 24 F6X C5 H4 SING N N 25 F6X N4 H5 SING N N 26 F6X N4 H6 SING N N 27 F6X "C2'" H7 SING N N 28 F6X "C3'" H8 SING N N 29 F6X OP2 HOP2 SING N N 30 F6X C3A H11 SING N N 31 F6X C3A H12 SING N N 32 F6X C3A H13 SING N N 33 F6X "O1'" H14 SING N N 34 F6X "N2'" H15 SING N N 35 F6X C2B H16 SING N N 36 F6X C2B H17 SING N N 37 F6X P OP3 SING N N 38 F6X OP3 HOP3 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 F6X InChI InChI 1.03 InChI=1S/C10H17N4O7P/c1-6(21-22(18,19)20)7(5-15)12-9(16)4-14-3-2-8(11)13-10(14)17/h2-3,6-7,15H,4-5H2,1H3,(H,12,16)(H2,11,13,17)(H2,18,19,20)/t6-,7-/m1/s1 F6X InChIKey InChI 1.03 BNPHLZWYYOHAKE-RNFRBKRXSA-N F6X SMILES_CANONICAL CACTVS 3.385 C[C@@H](O[P](O)(O)=O)[C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N F6X SMILES CACTVS 3.385 C[CH](O[P](O)(O)=O)[CH](CO)NC(=O)CN1C=CC(=NC1=O)N F6X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@H]([C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O F6X SMILES "OpenEye OEToolkits" 2.0.7 CC(C(CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O # _pdbx_chem_comp_identifier.comp_id F6X _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 "[(2~{R},3~{R})-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] 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 F6X 'Create component' 2020-04-03 PDBJ F6X 'Modify internal type' 2020-11-04 PDBJ F6X 'Modify linking type' 2020-11-04 PDBJ F6X 'Modify leaving atom flag' 2020-11-04 PDBJ F6X 'Modify linking type' 2020-11-18 PDBJ F6X 'Initial release' 2020-11-25 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 F6X "C1'" C 5.104 -1.125 1 F6X N1 N 9.002 2.625 2 F6X C6 C 7.702 3.375 3 F6X C5 C 7.702 4.875 4 F6X C4 C 9.002 5.625 5 F6X N3 N 10.301 4.875 6 F6X C2 C 10.301 3.375 7 F6X O2 O 11.600 2.625 8 F6X N4 N 9.002 7.125 9 F6X "C2'" C 6.404 -1.875 10 F6X "C3'" C 6.404 -3.375 11 F6X "O3'" O 5.104 -4.125 12 F6X OP1 O 3.604 -5.625 13 F6X P P 5.104 -5.625 14 F6X OP2 O 5.104 -7.125 15 F6X C3A C 7.702 -4.125 16 F6X "O1'" O 3.805 -1.875 17 F6X "N2'" N 7.702 -1.125 18 F6X C2A C 7.702 0.375 19 F6X O2A O 6.404 1.125 20 F6X C2B C 9.002 1.125 21 F6X OP3 O 6.604 -5.625 22 # 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 F6X OP2 P SINGLE NONE 1 F6X OP1 P DOUBLE NONE 2 F6X P "O3'" SINGLE NONE 3 F6X "C3'" C3A SINGLE BEGINWEDGE 4 F6X "O3'" "C3'" SINGLE NONE 5 F6X C5 C6 DOUBLE NONE 6 F6X C5 C4 SINGLE NONE 7 F6X C6 N1 SINGLE NONE 8 F6X "C3'" "C2'" SINGLE NONE 9 F6X C2B N1 SINGLE NONE 10 F6X C2B C2A SINGLE NONE 11 F6X "N2'" "C2'" SINGLE NONE 12 F6X "N2'" C2A SINGLE NONE 13 F6X N1 C2 SINGLE NONE 14 F6X C4 N4 SINGLE NONE 15 F6X C4 N3 DOUBLE NONE 16 F6X "C2'" "C1'" SINGLE BEGINWEDGE 17 F6X C2A O2A DOUBLE NONE 18 F6X C2 N3 SINGLE NONE 19 F6X C2 O2 DOUBLE NONE 20 F6X "C1'" "O1'" SINGLE NONE 21 F6X P OP3 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 F6X MurckoScaffold S1 scaffold 'O=c1nccc[nH]1' InChI=1S/C4H4N2O/c7-4-5-2-1-3-6-4/h1-3H,(H,5,6,7) VTGOHKSTWXHQJK-UHFFFAOYSA-N F6X amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N F6X peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N F6X 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 F6X pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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 F6X N1 S1 1 F6X C6 S1 1 F6X C5 S1 1 F6X C4 S1 1 F6X N3 S1 1 F6X C2 S1 1 F6X O2 S1 1 F6X "N2'" F1 1 F6X C2A F1 1 F6X O2A F1 1 F6X C2B F1 1 F6X O2A F2 1 F6X C2A F2 1 F6X C2B F2 1 F6X N1 F2 1 F6X "O3'" F3 1 F6X P F3 1 F6X OP1 F3 1 F6X OP2 F3 1 F6X H1 F3 1 F6X C5 F4 1 F6X C6 F4 1 F6X N1 F4 1 F6X C2 F4 1 F6X N3 F4 1 F6X C4 F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id F6X _pdbe_chem_comp_rdkit_properties.exactmw 336.083 _pdbe_chem_comp_rdkit_properties.amw 336.241 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 11 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 6 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 10 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22 _pdbe_chem_comp_rdkit_properties.NumAtoms 39 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 1 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500 _pdbe_chem_comp_rdkit_properties.NumRings 1 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 148.848 _pdbe_chem_comp_rdkit_properties.tpsa 177 _pdbe_chem_comp_rdkit_properties.CrippenClogP -1.680 _pdbe_chem_comp_rdkit_properties.CrippenMR 73.801 _pdbe_chem_comp_rdkit_properties.chi0v 10.988 _pdbe_chem_comp_rdkit_properties.chi1v 6.296 _pdbe_chem_comp_rdkit_properties.chi2v 2.014 _pdbe_chem_comp_rdkit_properties.chi3v 2.014 _pdbe_chem_comp_rdkit_properties.chi4v 1.205 _pdbe_chem_comp_rdkit_properties.chi0n 27.094 _pdbe_chem_comp_rdkit_properties.chi1n 12.902 _pdbe_chem_comp_rdkit_properties.chi2n 1.608 _pdbe_chem_comp_rdkit_properties.chi3n 1.608 _pdbe_chem_comp_rdkit_properties.chi4n 0.895 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.780 _pdbe_chem_comp_rdkit_properties.kappa1 5.392 _pdbe_chem_comp_rdkit_properties.kappa2 7.473 _pdbe_chem_comp_rdkit_properties.kappa3 5.916 _pdbe_chem_comp_rdkit_properties.Phi 1.831 # 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 F6X UniChem PDBe F6X F6X UniChem PubChem 155804425 # 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 F6X "C1'" -2.146 1.571 1.795 ETKDGv3 1 F6X N1 2.394 1.041 -0.979 ETKDGv3 2 F6X C6 2.526 -0.244 -1.610 ETKDGv3 3 F6X C5 3.221 -1.222 -1.021 ETKDGv3 4 F6X C4 3.866 -0.993 0.290 ETKDGv3 5 F6X N3 3.764 0.159 0.886 ETKDGv3 6 F6X C2 3.028 1.237 0.299 ETKDGv3 7 F6X O2 2.943 2.337 0.906 ETKDGv3 8 F6X N4 4.605 -2.045 0.911 ETKDGv3 9 F6X "C2'" -1.632 1.017 0.448 ETKDGv3 10 F6X "C3'" -1.367 -0.518 0.457 ETKDGv3 11 F6X "O3'" -2.561 -1.219 0.756 ETKDGv3 12 F6X OP1 -2.419 -2.984 -1.194 ETKDGv3 13 F6X P -3.262 -1.842 -0.673 ETKDGv3 14 F6X OP2 -4.812 -2.416 -0.318 ETKDGv3 15 F6X C3A -0.301 -0.925 1.481 ETKDGv3 16 F6X "O1'" -3.352 0.964 2.173 ETKDGv3 17 F6X "N2'" -0.417 1.735 0.047 ETKDGv3 18 F6X C2A 0.084 1.697 -1.296 ETKDGv3 19 F6X O2A -0.657 1.317 -2.243 ETKDGv3 20 F6X C2B 1.513 2.052 -1.571 ETKDGv3 21 F6X H1 -2.293 2.672 1.710 ETKDGv3 22 F6X H2 -1.395 1.410 2.597 ETKDGv3 23 F6X H3 2.049 -0.432 -2.565 ETKDGv3 24 F6X H4 3.307 -2.186 -1.506 ETKDGv3 25 F6X H5 4.697 -2.977 0.449 ETKDGv3 26 F6X H6 5.063 -1.894 1.838 ETKDGv3 27 F6X H7 -2.422 1.231 -0.303 ETKDGv3 28 F6X H8 -0.935 -0.797 -0.534 ETKDGv3 29 F6X HOP2 -5.297 -1.627 0.033 ETKDGv3 30 F6X H11 -0.055 -2.001 1.349 ETKDGv3 31 F6X H12 0.632 -0.341 1.338 ETKDGv3 32 F6X H13 -0.669 -0.786 2.518 ETKDGv3 33 F6X H14 -4.054 1.328 1.572 ETKDGv3 34 F6X H15 0.155 2.220 0.775 ETKDGv3 35 F6X H16 1.689 2.105 -2.668 ETKDGv3 36 F6X H17 1.728 3.061 -1.159 ETKDGv3 37 F6X OP3 -3.374 -0.636 -1.857 ETKDGv3 38 F6X HOP3 -3.843 -1.069 -2.614 ETKDGv3 39 #