data_X6H # _chem_comp.id X6H _chem_comp.name "(4aM,9M)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,5-dihydropyrimido[1,2-a]purine-6,10-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H14 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-10-31 _chem_comp.pdbx_modified_date 2023-07-28 _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 399.253 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X6H _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 8EVF _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 X6H "C1'" C1 C 0 1 N N R 60.059 6.323 -1.473 -0.348 0.762 0.058 "C1'" X6H 1 X6H C2 C2 C 0 1 N N N 57.110 3.778 -2.779 4.104 0.392 0.419 C2 X6H 2 X6H "C2'" C3 C 0 1 N N N 61.209 6.997 -0.750 -0.435 1.788 -1.089 "C2'" X6H 3 X6H "C3'" C4 C 0 1 N N S 60.708 8.432 -0.762 -1.932 1.788 -1.484 "C3'" X6H 4 X6H C4 C5 C 0 1 Y N N 59.334 4.457 -2.736 1.953 -0.270 -0.122 C4 X6H 5 X6H "C4'" C6 C 0 1 N N R 59.956 8.597 -2.056 -2.604 1.210 -0.212 "C4'" X6H 6 X6H C5 C7 C 0 1 Y N N 59.740 3.463 -3.586 2.433 -1.496 -0.601 C5 X6H 7 X6H "C5'" C8 C 0 1 N N N 60.894 9.065 -3.154 -3.949 0.568 -0.558 "C5'" X6H 8 X6H C6 C9 C 0 1 N N N 58.691 2.537 -4.080 3.824 -1.739 -0.556 C6 X6H 9 X6H C6A C10 C 0 1 N N N 54.828 3.267 -2.703 6.264 1.148 1.002 C6A X6H 10 X6H C7A C11 C 0 1 N N N 55.096 2.232 -3.596 6.805 -0.075 0.532 C7A X6H 11 X6H C8 C12 C 0 1 Y N N 61.456 4.708 -2.978 0.281 -1.505 -0.857 C8 X6H 12 X6H C8A C13 C 0 1 N N N 56.390 1.939 -4.050 5.985 -1.011 0.020 C8A X6H 13 X6H N1 N1 N 0 1 N N N 57.413 2.741 -3.649 4.630 -0.784 -0.039 N1 X6H 14 X6H N2 N2 N 0 1 N N N 55.863 4.037 -2.324 4.935 1.358 0.938 N2 X6H 15 X6H N3 N3 N 0 1 N N N 58.061 4.599 -2.346 2.809 0.629 0.371 N3 X6H 16 X6H N7 N4 N 0 1 Y N N 61.077 3.627 -3.731 1.363 -2.205 -1.036 N7 X6H 17 X6H N9 N5 N 0 1 Y N N 60.361 5.187 -2.371 0.595 -0.302 -0.295 N9 X6H 18 X6H "O3'" O1 O 0 1 N N N 59.700 8.639 0.228 -2.390 3.117 -1.743 "O3'" X6H 19 X6H "O4'" O2 O 0 1 N N N 59.446 7.297 -2.339 -1.663 0.212 0.241 "O4'" X6H 20 X6H "O5'" O3 O 0 1 N N N 62.103 8.317 -3.088 -4.599 0.148 0.643 "O5'" X6H 21 X6H O6 O4 O 0 1 N N N 58.973 1.612 -4.869 4.286 -2.789 -0.966 O6 X6H 22 X6H O6A O5 O 0 1 N N N 53.663 3.508 -2.276 6.997 2.005 1.462 O6A X6H 23 X6H OP3 O6 O 0 1 N Y N 63.861 10.151 -3.253 -7.157 0.459 0.118 OP3 X6H 24 X6H OP1 O7 O 0 1 N N N 64.529 7.821 -3.792 -6.005 -1.761 -0.223 OP1 X6H 25 X6H P P1 P 0 1 N N N 63.415 8.837 -3.843 -6.040 -0.570 0.655 P X6H 26 X6H OP2 O8 O 0 1 N N N 62.904 9.084 -5.336 -6.403 -1.020 2.157 OP2 X6H 27 X6H "H1'" H1 H 0 1 N N N 59.326 5.994 -0.722 -0.022 1.257 0.974 "H1'" X6H 28 X6H "H2'" H2 H 0 1 N N N 61.331 6.614 0.274 -0.132 2.775 -0.741 "H2'" X6H 29 X6H "H2''" H3 H 0 0 N N N 62.157 6.889 -1.297 0.183 1.473 -1.929 "H2''" X6H 30 X6H "H3'" H4 H 0 1 N N N 61.539 9.148 -0.682 -2.107 1.143 -2.345 "H3'" X6H 31 X6H "H4'" H5 H 0 1 N N N 59.141 9.324 -1.927 -2.733 1.987 0.541 "H4'" X6H 32 X6H "H5'" H6 H 0 1 N N N 61.115 10.134 -3.018 -4.576 1.295 -1.075 "H5'" X6H 33 X6H "H5''" H7 H 0 0 N N N 60.419 8.911 -4.134 -3.785 -0.294 -1.204 "H5''" X6H 34 X6H H1 H8 H 0 1 N N N 54.273 1.630 -3.953 7.870 -0.252 0.579 H1 X6H 35 X6H H8 H9 H 0 1 N N N 62.457 5.103 -2.890 -0.717 -1.827 -1.116 H8 X6H 36 X6H H10 H10 H 0 1 N N N 56.570 1.097 -4.702 6.392 -1.942 -0.345 H10 X6H 37 X6H H21 H11 H 0 1 N N N 55.710 4.805 -1.702 4.562 2.194 1.259 H21 X6H 38 X6H "HO3'" H12 H 0 0 N Y N 60.083 8.554 1.093 -1.934 3.555 -2.475 "HO3'" X6H 39 X6H HOP3 H13 H 0 0 N Y N 64.763 10.079 -2.963 -7.235 1.265 0.647 HOP3 X6H 40 X6H HOP2 H14 H 0 0 N N N 63.400 8.539 -5.935 -7.260 -1.461 2.240 HOP2 X6H 41 # 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 X6H O6 C6 DOUB N N 1 X6H C6 N1 SING N N 2 X6H C6 C5 SING N N 3 X6H C8A N1 SING N N 4 X6H C8A C7A DOUB N N 5 X6H P OP1 DOUB N N 6 X6H P OP3 SING N N 7 X6H P "O5'" SING N N 8 X6H N7 C5 SING Y N 9 X6H N7 C8 DOUB Y N 10 X6H N1 C2 SING N N 11 X6H C7A C6A SING N N 12 X6H C5 C4 DOUB Y N 13 X6H "C5'" "O5'" SING N N 14 X6H "C5'" "C4'" SING N N 15 X6H C8 N9 SING Y N 16 X6H C2 N3 DOUB N N 17 X6H C2 N2 SING N N 18 X6H C4 N9 SING Y N 19 X6H C4 N3 SING N N 20 X6H C6A N2 SING N N 21 X6H C6A O6A DOUB N N 22 X6H N9 "C1'" SING N N 23 X6H "O4'" "C4'" SING N N 24 X6H "O4'" "C1'" SING N N 25 X6H "C4'" "C3'" SING N N 26 X6H "C1'" "C2'" SING N N 27 X6H "C3'" "C2'" SING N N 28 X6H "C3'" "O3'" SING N N 29 X6H P OP2 SING N N 30 X6H "C1'" "H1'" SING N N 31 X6H "C2'" "H2'" SING N N 32 X6H "C2'" "H2''" SING N N 33 X6H "C3'" "H3'" SING N N 34 X6H "C4'" "H4'" SING N N 35 X6H "C5'" "H5'" SING N N 36 X6H "C5'" "H5''" SING N N 37 X6H C7A H1 SING N N 38 X6H C8 H8 SING N N 39 X6H C8A H10 SING N N 40 X6H N2 H21 SING N N 41 X6H "O3'" "HO3'" SING N N 42 X6H OP3 HOP3 SING N N 43 X6H OP2 HOP2 SING N N 44 # 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 X6H SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(CC1O)n1cnc2c1N=C1NC(=O)C=CN1C2=O" X6H InChI InChI 1.06 "InChI=1S/C13H14N5O8P/c19-6-3-9(26-7(6)4-25-27(22,23)24)18-5-14-10-11(18)16-13-15-8(20)1-2-17(13)12(10)21/h1-2,5-7,9,19H,3-4H2,(H,15,16,20)(H2,22,23,24)/t6-,7+,9+/m0/s1" X6H InChIKey InChI 1.06 NJGWJRXLEBYAKE-LKEWCRSYSA-N X6H SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC(=O)NC4=Nc23" X6H SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC(=O)NC4=Nc23" X6H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C4NC(=O)C=CN4C2=O" X6H SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4NC(=O)C=CN4C2=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 X6H "SYSTEMATIC NAME" ACDLabs 12.01 "(4aM,9M)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,5-dihydropyrimido[1,2-a]purine-6,10-dione" X6H "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[6,10-bis(oxidanylidene)-5~{H}-pyrimido[1,2-a]purin-3-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 X6H "Create component" 2022-10-31 RCSB X6H "Initial release" 2023-08-02 RCSB #