data_VF5 # _chem_comp.id VF5 _chem_comp.name "[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O16 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-13 _chem_comp.pdbx_modified_date 2022-05-27 _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 585.145 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VF5 _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 7OIW _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 VF5 P P1 P 0 1 N N N -36.147 -4.020 -12.268 -2.696 -1.001 1.161 P VF5 1 VF5 C1 C1 C 0 1 Y N N -37.091 3.463 -10.100 4.675 1.768 -0.089 C1 VF5 2 VF5 O1 O1 O 0 1 N N N -36.802 -2.910 -11.332 -1.243 -0.986 0.467 O1 VF5 3 VF5 C2 C2 C 0 1 Y N N -37.918 3.689 -9.020 4.957 2.754 0.864 C2 VF5 4 VF5 O2 O2 O 0 1 N N N -36.286 -3.537 -13.713 -3.109 -2.400 1.409 O2 VF5 5 VF5 C3 C3 C 0 1 Y N N -38.573 1.858 -9.895 3.172 1.716 1.523 C3 VF5 6 VF5 O3 O3 O 0 1 N N N -34.761 -4.329 -11.853 -2.632 -0.204 2.558 O3 VF5 7 VF5 C4 C4 C 0 1 N N R -36.957 1.615 -11.850 2.862 0.022 -0.324 C4 VF5 8 VF5 O4 O4 O 0 1 N N N -37.090 -5.293 -12.109 -3.763 -0.291 0.186 O4 VF5 9 VF5 C5 C5 C 0 1 N N R -36.954 -0.704 -12.265 1.109 -1.423 0.124 C5 VF5 10 VF5 O5 O5 O 0 1 N N N -38.199 -7.354 -13.018 -5.927 -1.651 -0.430 O5 VF5 11 VF5 C6 C6 C 0 1 N N N -37.733 -1.892 -11.758 -0.103 -1.633 1.035 C6 VF5 12 VF5 O6 O6 O 0 1 N N N -35.669 -7.106 -13.194 -5.905 -0.016 1.493 O6 VF5 13 VF5 C7 C7 C 0 1 N N R -35.680 -0.398 -11.488 2.357 -2.125 0.708 C7 VF5 14 VF5 O7 O7 O 0 1 N N N -36.789 -7.450 -10.940 -5.844 0.945 -0.841 O7 VF5 15 VF5 O8 O8 O 0 1 N N N -37.920 -7.210 -8.731 -6.940 3.093 -1.888 O8 VF5 16 VF5 O9 O9 O 0 1 N N N -37.171 -9.450 -9.489 -8.303 0.848 -1.766 O9 VF5 17 VF5 O10 O10 O 0 1 N N N -39.143 -8.357 -10.623 -7.733 2.155 0.317 O10 VF5 18 VF5 N N1 N 0 1 N N N -34.892 6.153 -10.100 7.305 2.228 -2.437 N VF5 19 VF5 C C8 C 0 1 N N N -35.875 5.304 -9.790 6.518 2.407 -1.327 C VF5 20 VF5 O O11 O 0 1 N N N -37.763 0.489 -12.156 1.488 -0.030 0.095 O VF5 21 VF5 C8 C9 C 0 1 N N R -35.525 1.116 -11.647 3.518 -1.315 0.079 C8 VF5 22 VF5 C9 C10 C 0 1 N N N -37.702 4.864 -8.232 6.087 3.582 0.667 C9 VF5 23 VF5 N1 N2 N 0 1 N N N -36.064 4.217 -10.535 5.471 1.631 -1.156 N1 VF5 24 VF5 N2 N3 N 0 1 Y N N -38.848 2.669 -8.899 4.003 2.671 1.823 N2 VF5 25 VF5 N3 N4 N 0 1 Y N N -37.519 2.282 -10.664 3.544 1.133 0.347 N3 VF5 26 VF5 N4 N5 N 0 1 N N N -36.645 5.617 -8.702 6.844 3.384 -0.434 N4 VF5 27 VF5 O11 O12 O 0 1 N N N -34.526 -0.996 -12.133 2.402 -3.485 0.263 O11 VF5 28 VF5 O12 O13 O 0 1 N N N -32.431 0.359 -12.315 4.982 -4.133 0.059 O12 VF5 29 VF5 O13 O14 O 0 1 N N N -33.501 -0.330 -14.423 3.400 -4.389 -1.917 O13 VF5 30 VF5 O14 O15 O 0 1 N N N -34.707 1.290 -12.826 3.910 -1.999 -1.137 O14 VF5 31 VF5 O15 O16 O 0 1 N N N -38.336 5.225 -7.243 6.370 4.454 1.471 O15 VF5 32 VF5 P1 P2 P 0 1 N N N -36.894 -6.845 -12.409 -5.372 -0.248 0.132 P1 VF5 33 VF5 P2 P3 P 0 1 N N N -37.828 -8.142 -9.947 -7.216 1.769 -1.015 P2 VF5 34 VF5 P3 P4 P 0 1 N N N -33.744 0.056 -13.018 3.695 -3.564 -0.724 P3 VF5 35 VF5 H1 H1 H 0 1 N N N -39.122 0.948 -10.089 2.315 1.431 2.114 H1 VF5 36 VF5 H2 H2 H 0 1 N N N -34.170 -4.170 -12.579 -2.367 0.722 2.471 H2 VF5 37 VF5 H3 H3 H 0 1 N N N -36.962 2.319 -12.695 2.918 0.152 -1.404 H3 VF5 38 VF5 H4 H4 H 0 1 N N N -36.690 -0.877 -13.319 0.898 -1.785 -0.883 H4 VF5 39 VF5 H5 H5 H 0 1 N N N -38.017 -7.781 -13.847 -5.617 -1.868 -1.320 H5 VF5 40 VF5 H6 H6 H 0 1 N N N -38.362 -1.587 -10.909 0.104 -1.209 2.017 H6 VF5 41 VF5 H7 H7 H 0 1 N N N -38.370 -2.287 -12.563 -0.302 -2.700 1.134 H7 VF5 42 VF5 H8 H8 H 0 1 N N N -35.772 -0.685 -10.430 2.374 -2.059 1.796 H8 VF5 43 VF5 H9 H9 H 0 1 N N N -38.819 -6.925 -8.617 -7.724 3.639 -2.034 H9 VF5 44 VF5 H10 H10 H 0 1 N N N -37.729 -10.183 -9.721 -8.031 0.557 -2.647 H10 VF5 45 VF5 H11 H11 H 0 1 N N N -34.303 5.970 -10.888 8.081 2.793 -2.577 H11 VF5 46 VF5 H12 H12 H 0 1 N N N -34.744 6.971 -9.545 7.086 1.537 -3.081 H12 VF5 47 VF5 H13 H13 H 0 1 N N N -35.071 1.565 -10.751 4.349 -1.178 0.770 H13 VF5 48 VF5 H14 H14 H 0 1 N N N -36.424 6.458 -8.209 7.624 3.940 -0.591 H14 VF5 49 VF5 H15 H15 H 0 1 N N N -31.711 0.239 -12.923 5.791 -4.146 -0.471 H15 VF5 50 # # 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 VF5 O13 P3 DOUB N N 1 VF5 O2 P DOUB N N 2 VF5 O6 P1 DOUB N N 3 VF5 P3 O14 SING N N 4 VF5 P3 O12 SING N N 5 VF5 P3 O11 SING N N 6 VF5 O5 P1 SING N N 7 VF5 O14 C8 SING N N 8 VF5 P1 O4 SING N N 9 VF5 P1 O7 SING N N 10 VF5 P O4 SING N N 11 VF5 P O3 SING N N 12 VF5 P O1 SING N N 13 VF5 C5 O SING N N 14 VF5 C5 C6 SING N N 15 VF5 C5 C7 SING N N 16 VF5 O C4 SING N N 17 VF5 O11 C7 SING N N 18 VF5 C4 C8 SING N N 19 VF5 C4 N3 SING N N 20 VF5 C6 O1 SING N N 21 VF5 C8 C7 SING N N 22 VF5 O7 P2 SING N N 23 VF5 N3 C1 SING Y N 24 VF5 N3 C3 SING Y N 25 VF5 O10 P2 DOUB N N 26 VF5 N1 C1 SING N N 27 VF5 N1 C DOUB N N 28 VF5 N C SING N N 29 VF5 C1 C2 DOUB Y N 30 VF5 P2 O9 SING N N 31 VF5 P2 O8 SING N N 32 VF5 C3 N2 DOUB Y N 33 VF5 C N4 SING N N 34 VF5 C2 N2 SING Y N 35 VF5 C2 C9 SING N N 36 VF5 N4 C9 SING N N 37 VF5 C9 O15 DOUB N N 38 VF5 C3 H1 SING N N 39 VF5 O3 H2 SING N N 40 VF5 C4 H3 SING N N 41 VF5 C5 H4 SING N N 42 VF5 O5 H5 SING N N 43 VF5 C6 H6 SING N N 44 VF5 C6 H7 SING N N 45 VF5 C7 H8 SING N N 46 VF5 O8 H9 SING N N 47 VF5 O9 H10 SING N N 48 VF5 N H11 SING N N 49 VF5 N H12 SING N N 50 VF5 C8 H13 SING N N 51 VF5 N4 H14 SING N N 52 VF5 O12 H15 SING N N 53 # # 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 VF5 InChI InChI 1.03 "InChI=1S/C10H15N5O16P4/c11-10-13-7-4(8(16)14-10)12-2-15(7)9-6-5(28-34(22,23)29-6)3(27-9)1-26-33(20,21)31-35(24,25)30-32(17,18)19/h2-3,5-6,9H,1H2,(H,20,21)(H,22,23)(H,24,25)(H2,17,18,19)(H3,11,13,14,16)/t3-,5-,6-,9-/m1/s1" VF5 InChIKey InChI 1.03 RSYPFLCCTRWIKG-UUOKFMHZSA-N VF5 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@H]4O[P](O)(=O)O[C@@H]34" VF5 SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH]4O[P](O)(=O)O[CH]34" VF5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O4)O)N=C(NC2=O)N" VF5 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C4C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O4)O)N=C(NC2=O)N" # _pdbx_chem_comp_identifier.comp_id VF5 _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 "[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 VF5 "Create component" 2021-05-13 PDBE VF5 "Initial release" 2022-06-01 RCSB ##