data_ZDA # _chem_comp.id ZDA _chem_comp.name "2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N5 O11 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-10-29 _chem_comp.pdbx_modified_date 2020-06-17 _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 475.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZDA _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 4WP8 _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 ZDA "C2'" C1 C 0 1 N N N 56.928 -1.447 50.611 2.368 -0.820 -0.658 "C2'" ZDA 1 ZDA "C5'" C2 C 0 1 N N N 59.776 -2.575 52.656 1.766 -4.010 0.756 "C5'" ZDA 2 ZDA "C4'" C3 C 0 1 N N R 58.280 -2.067 52.434 1.744 -2.499 0.996 "C4'" ZDA 3 ZDA "O4'" O1 O 0 1 N N N 58.159 -0.767 52.529 3.078 -2.022 1.235 "O4'" ZDA 4 ZDA "C1'" C4 C 0 1 N N R 56.779 -0.590 51.912 3.160 -0.696 0.669 "C1'" ZDA 5 ZDA N9 N1 N 0 1 Y N N 56.609 0.838 51.899 4.555 -0.333 0.404 N9 ZDA 6 ZDA C8 C5 C 0 1 Y N N 57.480 1.786 51.484 5.604 -1.196 0.288 C8 ZDA 7 ZDA N7 N2 N 0 1 Y N N 56.891 2.984 51.587 6.700 -0.533 0.053 N7 ZDA 8 ZDA C5 C6 C 0 1 Y N N 55.624 2.795 52.058 6.423 0.792 0.004 C5 ZDA 9 ZDA C6 C7 C 0 1 Y N N 54.527 3.623 52.354 7.186 1.953 -0.210 C6 ZDA 10 ZDA N6 N3 N 0 1 N N N 54.617 5.061 52.199 8.548 1.874 -0.438 N6 ZDA 11 ZDA N1 N4 N 0 1 Y N N 53.378 3.093 52.805 6.567 3.129 -0.190 N1 ZDA 12 ZDA C2 C8 C 0 1 Y N N 53.267 1.765 52.977 5.267 3.215 0.026 C2 ZDA 13 ZDA N3 N5 N 0 1 Y N N 54.278 0.942 52.704 4.514 2.155 0.231 N3 ZDA 14 ZDA C4 C9 C 0 1 Y N N 55.459 1.443 52.230 5.043 0.936 0.222 C4 ZDA 15 ZDA "C3'" C10 C 0 1 N N S 57.747 -2.418 50.928 1.217 -1.777 -0.260 "C3'" ZDA 16 ZDA "O3'" O2 O 0 1 N N N 57.039 -3.650 50.934 0.035 -1.036 0.048 "O3'" ZDA 17 ZDA PA P1 P 0 1 N N N 57.231 -4.685 49.723 -1.359 -1.248 -0.729 PA ZDA 18 ZDA O1A O3 O 0 1 N N N 56.430 -4.244 48.528 -1.749 -2.674 -0.664 O1A ZDA 19 ZDA O2A O4 O 0 1 N N N 56.844 -6.067 50.246 -1.188 -0.809 -2.269 O2A ZDA 20 ZDA O3A O5 O 0 1 N N N 58.755 -4.589 49.357 -2.501 -0.347 -0.038 O3A ZDA 21 ZDA PB P2 P 0 1 N N N 59.481 -5.007 48.025 -4.111 -0.388 -0.038 PB ZDA 22 ZDA O2B O6 O 0 1 N N N 60.946 -4.733 48.208 -4.619 -1.505 1.005 O2B ZDA 23 ZDA O1B O7 O 0 1 N N N 58.929 -4.342 46.785 -4.596 -0.724 -1.395 O1B ZDA 24 ZDA O3B O8 O 0 1 N N N 59.227 -6.590 48.024 -4.684 1.052 0.396 O3B ZDA 25 ZDA PG P3 P 0 1 N N N 58.401 -7.478 46.964 -6.130 1.754 0.304 PG ZDA 26 ZDA O2G O9 O 0 1 N N N 58.003 -8.718 47.735 -7.061 1.226 1.507 O2G ZDA 27 ZDA O3G O10 O 0 1 N N N 57.161 -6.726 46.484 -5.960 3.351 0.419 O3G ZDA 28 ZDA O1G O11 O 0 1 N N N 59.326 -7.767 45.804 -6.760 1.417 -0.992 O1G ZDA 29 ZDA H1 H1 H 0 1 N N N 57.348 -0.840 49.796 1.978 0.148 -0.970 H1 ZDA 30 ZDA H2 H2 H 0 1 N N N 55.953 -1.851 50.302 2.986 -1.260 -1.441 H2 ZDA 31 ZDA H3 H3 H 0 1 N N N 60.102 -2.323 53.676 2.151 -4.512 1.644 H3 ZDA 32 ZDA H4 H4 H 0 1 N N N 59.817 -3.665 52.517 0.755 -4.360 0.550 H4 ZDA 33 ZDA H5 H5 H 0 1 N N N 60.441 -2.087 51.928 2.408 -4.233 -0.095 H5 ZDA 34 ZDA H6 H6 H 0 1 N N N 57.632 -2.597 53.147 1.109 -2.269 1.852 H6 ZDA 35 ZDA H7 H7 H 0 1 N N N 56.027 -1.061 52.562 2.691 0.033 1.329 H7 ZDA 36 ZDA H8 H8 H 0 1 N N N 58.484 1.606 51.129 5.537 -2.270 0.378 H8 ZDA 37 ZDA H9 H9 H 0 1 N N N 53.750 5.481 52.469 8.988 1.010 -0.451 H9 ZDA 38 ZDA H10 H10 H 0 1 N N N 55.352 5.413 52.778 9.064 2.683 -0.584 H10 ZDA 39 ZDA H11 H11 H 0 1 N N N 52.338 1.356 53.345 4.804 4.191 0.035 H11 ZDA 40 ZDA H12 H12 H 0 1 N N N 58.621 -2.472 50.262 1.022 -2.492 -1.059 H12 ZDA 41 ZDA H13 H13 H 0 1 N N N 56.143 -6.423 49.712 -0.932 0.116 -2.388 H13 ZDA 42 ZDA H14 H14 H 0 1 N N N 61.257 -4.184 47.498 -4.337 -1.349 1.916 H14 ZDA 43 ZDA H15 H15 H 0 1 N N N 58.415 -9.480 47.345 -6.709 1.412 2.388 H15 ZDA 44 ZDA H16 H16 H 0 1 N N N 57.217 -6.588 45.546 -6.793 3.840 0.371 H16 ZDA 45 # # 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 ZDA O1G PG DOUB N N 1 ZDA O3G PG SING N N 2 ZDA O1B PB DOUB N N 3 ZDA PG O2G SING N N 4 ZDA PG O3B SING N N 5 ZDA O3B PB SING N N 6 ZDA PB O2B SING N N 7 ZDA PB O3A SING N N 8 ZDA O1A PA DOUB N N 9 ZDA O3A PA SING N N 10 ZDA PA O2A SING N N 11 ZDA PA "O3'" SING N N 12 ZDA "C2'" "C3'" SING N N 13 ZDA "C2'" "C1'" SING N N 14 ZDA "C3'" "O3'" SING N N 15 ZDA "C3'" "C4'" SING N N 16 ZDA C8 N7 DOUB Y N 17 ZDA C8 N9 SING Y N 18 ZDA N7 C5 SING Y N 19 ZDA N9 "C1'" SING N N 20 ZDA N9 C4 SING Y N 21 ZDA "C1'" "O4'" SING N N 22 ZDA C5 C4 DOUB Y N 23 ZDA C5 C6 SING Y N 24 ZDA N6 C6 SING N N 25 ZDA C4 N3 SING Y N 26 ZDA C6 N1 DOUB Y N 27 ZDA "C4'" "O4'" SING N N 28 ZDA "C4'" "C5'" SING N N 29 ZDA N3 C2 DOUB Y N 30 ZDA N1 C2 SING Y N 31 ZDA "C2'" H1 SING N N 32 ZDA "C2'" H2 SING N N 33 ZDA "C5'" H3 SING N N 34 ZDA "C5'" H4 SING N N 35 ZDA "C5'" H5 SING N N 36 ZDA "C4'" H6 SING N N 37 ZDA "C1'" H7 SING N N 38 ZDA C8 H8 SING N N 39 ZDA N6 H9 SING N N 40 ZDA N6 H10 SING N N 41 ZDA C2 H11 SING N N 42 ZDA "C3'" H12 SING N N 43 ZDA O2A H13 SING N N 44 ZDA O2B H14 SING N N 45 ZDA O2G H15 SING N N 46 ZDA O3G H16 SING N N 47 # # 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 ZDA SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OC3C(OC(n2cnc1c(ncnc12)N)C3)C" ZDA InChI InChI 1.03 "InChI=1S/C10H16N5O11P3/c1-5-6(24-28(19,20)26-29(21,22)25-27(16,17)18)2-7(23-5)15-4-14-8-9(11)12-3-13-10(8)15/h3-7H,2H2,1H3,(H,19,20)(H,21,22)(H2,11,12,13)(H2,16,17,18)/t5-,6+,7-/m1/s1" ZDA InChIKey InChI 1.03 ZJGUOEYCABTFNH-DSYKOEDSSA-N ZDA SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](C[C@@H]1O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23" ZDA SMILES CACTVS 3.385 "C[CH]1O[CH](C[CH]1O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23" ZDA SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C[C@@H]1[C@H](C[C@@H](O1)n2cnc3c2ncnc3N)OP(=O)(O)OP(=O)(O)OP(=O)(O)O" ZDA SMILES "OpenEye OEToolkits" 1.9.2 "CC1C(CC(O1)n2cnc3c2ncnc3N)OP(=O)(O)OP(=O)(O)OP(=O)(O)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 ZDA "SYSTEMATIC NAME" ACDLabs 12.01 "2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate)" ZDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-methyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] 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 ZDA "Create component" 2014-10-29 PDBJ ZDA "Initial release" 2015-09-02 RCSB ZDA "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id ZDA _pdbx_chem_comp_synonyms.name "2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##