data_6U4 # _chem_comp.id 6U4 _chem_comp.name "[[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N5 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 2-oxo-dATP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-06-24 _chem_comp.pdbx_modified_date 2021-03-01 _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 507.181 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6U4 _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 5GHJ _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.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 6U4 PG P1 P 0 1 N N N -7.076 -2.247 -9.336 6.411 1.972 0.679 PG 6U4 1 6U4 O3G O1 O 0 1 N N N -6.633 -0.808 -9.347 6.164 2.936 1.945 O3G 6U4 2 6U4 O2G O2 O 0 1 N N N -7.066 -2.929 -7.982 7.027 2.830 -0.537 O2G 6U4 3 6U4 O1G O3 O 0 1 N N N -8.336 -2.479 -10.154 7.357 0.898 1.054 O1G 6U4 4 6U4 PB P2 P 0 1 N N N -5.041 -4.313 -9.905 4.613 0.026 -0.651 PB 6U4 5 6U4 O1B O4 O 0 1 N N N -5.923 -5.483 -9.601 5.434 -1.128 -0.224 O1B 6U4 6 6U4 O2B O5 O 0 1 N N N -3.916 -3.976 -8.964 4.880 0.327 -2.210 O2B 6U4 7 6U4 O3B O6 O 0 1 N N N -5.931 -2.982 -10.210 5.012 1.320 0.221 O3B 6U4 8 6U4 PA P3 P 0 1 N N N -5.068 -4.841 -12.797 2.153 -1.627 -0.647 PA 6U4 9 6U4 O2A O7 O 0 1 N N N -6.096 -5.918 -12.705 1.880 -1.836 -2.220 O2A 6U4 10 6U4 O1A O8 O 0 1 N N N -5.411 -3.521 -13.431 2.865 -2.808 -0.109 O1A 6U4 11 6U4 O3A O9 O 0 1 N N N -4.394 -4.536 -11.365 3.055 -0.311 -0.428 O3A 6U4 12 6U4 "O5'" O10 O 0 1 N N N -3.760 -5.402 -13.509 0.750 -1.450 0.122 "O5'" 6U4 13 6U4 "C5'" C1 C 0 1 N N N -3.798 -5.855 -14.870 -0.228 -2.489 0.206 "C5'" 6U4 14 6U4 "C4'" C2 C 0 1 N N R -3.264 -7.269 -14.882 -1.435 -1.990 1.003 "C4'" 6U4 15 6U4 "O4'" O11 O 0 1 N N N -3.539 -7.814 -16.170 -2.156 -0.990 0.249 "O4'" 6U4 16 6U4 "C3'" C3 C 0 1 N N S -1.762 -7.312 -14.709 -2.451 -3.134 1.214 "C3'" 6U4 17 6U4 "O3'" O12 O 0 1 N N N -1.399 -8.571 -14.133 -2.291 -3.712 2.511 "O3'" 6U4 18 6U4 "C2'" C4 C 0 1 N N N -1.272 -7.276 -16.150 -3.827 -2.441 1.095 "C2'" 6U4 19 6U4 "C1'" C5 C 0 1 N N R -2.351 -8.100 -16.871 -3.480 -0.960 0.827 "C1'" 6U4 20 6U4 N9 N1 N 0 1 N N N -2.459 -7.681 -18.288 -4.435 -0.376 -0.118 N9 6U4 21 6U4 C8 C6 C 0 1 N N N -2.930 -6.502 -18.730 -4.644 -0.776 -1.407 C8 6U4 22 6U4 N7 N2 N 0 1 N N N -2.831 -6.462 -20.084 -5.562 -0.041 -1.959 N7 6U4 23 6U4 C5 C7 C 0 1 N N N -2.301 -7.652 -20.461 -6.002 0.879 -1.062 C5 6U4 24 6U4 C6 C8 C 0 1 N N N -1.952 -8.185 -21.696 -6.953 1.902 -1.099 C6 6U4 25 6U4 N6 N3 N 0 1 N N N -2.137 -7.483 -22.841 -7.679 2.141 -2.234 N6 6U4 26 6U4 N1 N4 N 0 1 N N N -1.381 -9.402 -21.706 -7.141 2.655 0.023 N1 6U4 27 6U4 C2 C9 C 0 1 N N N -1.208 -10.141 -20.578 -6.424 2.413 1.134 C2 6U4 28 6U4 N3 N5 N 0 1 N N N -1.545 -9.655 -19.361 -5.517 1.446 1.186 N3 6U4 29 6U4 C4 C10 C 0 1 N N N -2.067 -8.409 -19.321 -5.285 0.668 0.133 C4 6U4 30 6U4 O2 O13 O 0 1 N N N -0.750 -11.289 -20.668 -6.613 3.103 2.124 O2 6U4 31 6U4 H1 H1 H 0 1 N N N -7.234 -0.295 -9.874 6.966 3.364 2.275 H1 6U4 32 6U4 H2 H2 H 0 1 N N N -7.878 -3.407 -7.862 6.459 3.553 -0.835 H2 6U4 33 6U4 H3 H3 H 0 1 N N N -3.909 -4.595 -8.244 4.373 1.073 -2.559 H3 6U4 34 6U4 H4 H4 H 0 1 N N N -6.909 -5.614 -13.090 1.416 -1.099 -2.640 H4 6U4 35 6U4 H5 H5 H 0 1 N N N -3.170 -5.209 -15.501 -0.546 -2.770 -0.798 H5 6U4 36 6U4 H6 H6 H 0 1 N N N -4.832 -5.839 -15.244 0.204 -3.355 0.706 H6 6U4 37 6U4 H7 H7 H 0 1 N N N -3.749 -7.859 -14.090 -1.114 -1.585 1.963 H7 6U4 38 6U4 H8 H8 H 0 1 N N N -1.392 -6.451 -14.133 -2.336 -3.894 0.441 H8 6U4 39 6U4 H9 H9 H 0 1 N N N -1.700 -8.606 -13.232 -2.905 -4.437 2.697 H9 6U4 40 6U4 H10 H10 H 0 1 N N N -0.280 -7.742 -16.247 -4.394 -2.858 0.263 H10 6U4 41 6U4 H11 H11 H 0 1 N N N -1.232 -6.246 -16.534 -4.386 -2.542 2.025 H11 6U4 42 6U4 H12 H12 H 0 1 N N N -2.098 -9.169 -16.809 -3.474 -0.397 1.760 H12 6U4 43 6U4 H13 H13 H 0 1 N N N -3.324 -5.712 -18.108 -4.122 -1.586 -1.896 H13 6U4 44 6U4 H14 H14 H 0 1 N N N -2.573 -6.608 -22.630 -7.536 1.599 -3.024 H14 6U4 45 6U4 H15 H15 H 0 1 N N N -1.252 -7.318 -23.277 -8.336 2.855 -2.247 H15 6U4 46 6U4 H16 H16 H 0 1 N N N -1.071 -9.779 -22.579 -7.797 3.370 0.019 H16 6U4 47 # # 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 6U4 N6 C6 SING N N 1 6U4 N1 C6 SING N N 2 6U4 N1 C2 SING N N 3 6U4 C6 C5 DOUB N N 4 6U4 O2 C2 DOUB N N 5 6U4 C2 N3 SING N N 6 6U4 C5 N7 SING N N 7 6U4 C5 C4 SING N N 8 6U4 N7 C8 DOUB N N 9 6U4 N3 C4 DOUB N N 10 6U4 C4 N9 SING N N 11 6U4 C8 N9 SING N N 12 6U4 N9 "C1'" SING N N 13 6U4 "C1'" "O4'" SING N N 14 6U4 "C1'" "C2'" SING N N 15 6U4 "O4'" "C4'" SING N N 16 6U4 "C2'" "C3'" SING N N 17 6U4 "C4'" "C5'" SING N N 18 6U4 "C4'" "C3'" SING N N 19 6U4 "C5'" "O5'" SING N N 20 6U4 "C3'" "O3'" SING N N 21 6U4 "O5'" PA SING N N 22 6U4 O1A PA DOUB N N 23 6U4 PA O2A SING N N 24 6U4 PA O3A SING N N 25 6U4 O3A PB SING N N 26 6U4 O3B PB SING N N 27 6U4 O3B PG SING N N 28 6U4 O1G PG DOUB N N 29 6U4 PB O1B DOUB N N 30 6U4 PB O2B SING N N 31 6U4 O3G PG SING N N 32 6U4 PG O2G SING N N 33 6U4 O3G H1 SING N N 34 6U4 O2G H2 SING N N 35 6U4 O2B H3 SING N N 36 6U4 O2A H4 SING N N 37 6U4 "C5'" H5 SING N N 38 6U4 "C5'" H6 SING N N 39 6U4 "C4'" H7 SING N N 40 6U4 "C3'" H8 SING N N 41 6U4 "O3'" H9 SING N N 42 6U4 "C2'" H10 SING N N 43 6U4 "C2'" H11 SING N N 44 6U4 "C1'" H12 SING N N 45 6U4 C8 H13 SING N N 46 6U4 N6 H14 SING N N 47 6U4 N6 H15 SING N N 48 6U4 N1 H16 SING N N 49 # # 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 6U4 InChI InChI 1.03 "InChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1" 6U4 InChIKey InChI 1.03 UOACBPRDWRDEHJ-KVQBGUIXSA-N 6U4 SMILES_CANONICAL CACTVS 3.385 "NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1" 6U4 SMILES CACTVS 3.385 "NC1=C2N=CN([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1" 6U4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" 6U4 SMILES "OpenEye OEToolkits" 2.0.5 "C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id 6U4 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.5 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},5~{R})-5-(6-azanyl-2-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-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 6U4 "Create component" 2016-06-24 PDBJ 6U4 "Other modification" 2016-06-24 PDBJ 6U4 "Initial release" 2017-01-04 RCSB 6U4 "Other modification" 2019-09-06 PDBJ 6U4 "Other modification" 2019-09-17 PDBJ 6U4 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 6U4 _pdbx_chem_comp_synonyms.name 2-oxo-dATP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##