data_A2D # _chem_comp.id A2D _chem_comp.name "BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 N10 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "BIS(ADENOSINE)-5'-DIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-10-25 _chem_comp.pdbx_modified_date 2021-03-01 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 676.427 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A2D _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 A2D PA PA P 0 1 N N S 14.306 7.549 13.388 4.853 3.286 -1.557 PA A2D 1 A2D O1A O1A O 0 1 N N N 14.649 8.597 14.574 3.237 3.311 -1.628 O1A A2D 2 A2D O2A O2A O 0 1 N N N 13.697 6.304 13.461 5.417 3.560 -0.193 O2A A2D 3 A2D O3A O3A O 0 1 N N N 13.678 8.439 12.658 5.239 1.840 -2.168 O3A A2D 4 A2D PB PB P 0 1 N N R 12.904 9.645 12.912 4.948 0.346 -1.624 PB A2D 5 A2D O1B O1B O 0 1 N N N 11.422 9.477 12.862 5.526 0.037 -0.274 O1B A2D 6 A2D O2B O2B O 0 1 N N N 13.409 10.767 13.768 3.338 0.218 -1.723 O2B A2D 7 A2D O5D O5*A O 0 1 N N N 15.729 7.529 12.628 5.332 4.309 -2.716 O5D A2D 8 A2D C5D C5*A C 0 1 N N N 16.702 6.539 12.946 4.862 4.146 -4.043 C5D A2D 9 A2D C4D C4*A C 0 1 N N R 17.860 7.216 13.655 5.465 5.234 -4.920 C4D A2D 10 A2D O4D O4*A O 0 1 N N N 18.258 8.362 12.910 6.903 5.079 -4.915 O4D A2D 11 A2D C3D C3*A C 0 1 N N S 17.509 7.712 15.053 5.025 5.136 -6.377 C3D A2D 12 A2D O3D O3*A O 0 1 N N N 18.279 6.961 15.994 5.101 6.433 -6.970 O3D A2D 13 A2D C2D C2*A C 0 1 N N R 17.869 9.195 15.059 6.093 4.243 -6.977 C2D A2D 14 A2D O2D O2*A O 0 1 N N N 18.548 9.601 16.257 6.218 4.394 -8.377 O2D A2D 15 A2D C1D C1*A C 0 1 N N R 18.780 9.292 13.847 7.335 4.720 -6.242 C1D A2D 16 A2D N9A N9A N 0 1 Y N N 18.895 10.622 13.204 8.399 3.722 -6.160 N9A A2D 17 A2D C8A C8A C 0 1 Y N N 17.931 11.479 12.822 8.523 2.750 -5.202 C8A A2D 18 A2D N7A N7A N 0 1 Y N N 18.525 12.558 12.267 9.587 1.997 -5.391 N7A A2D 19 A2D C5A C5A C 0 1 Y N N 19.874 12.364 12.291 10.180 2.503 -6.520 C5A A2D 20 A2D C6A C6A C 0 1 Y N N 21.002 13.092 11.875 11.326 2.141 -7.221 C6A A2D 21 A2D N6A N6A N 0 1 N N N 20.907 14.308 11.279 12.120 1.064 -6.790 N6A A2D 22 A2D N1A N1A N 0 1 Y N N 22.228 12.556 12.072 11.670 2.842 -8.328 N1A A2D 23 A2D C2A C2A C 0 1 Y N N 22.402 11.361 12.651 10.866 3.869 -8.694 C2A A2D 24 A2D N3A N3A N 0 1 Y N N 21.354 10.640 13.059 9.737 4.314 -8.100 N3A A2D 25 A2D C4A C4A C 0 1 Y N N 20.089 11.126 12.882 9.456 3.577 -7.014 C4A A2D 26 A2D O5E O5*B O 0 1 N N N 13.267 10.410 11.563 5.497 -0.548 -2.856 O5E A2D 27 A2D C5E C5*B C 0 1 N N N 13.666 9.672 10.419 6.882 -0.513 -3.152 C5E A2D 28 A2D C4E C4*B C 0 1 N N R 15.126 9.934 10.140 7.294 -1.849 -3.743 C4E A2D 29 A2D O4E O4*B O 0 1 N N N 15.853 8.724 10.026 6.588 -2.075 -4.974 O4E A2D 30 A2D C3E C3*B C 0 1 N N S 15.275 10.609 8.812 8.767 -1.920 -4.110 C3E A2D 31 A2D O3E O3*B O 0 1 N N N 16.490 11.327 8.890 9.581 -2.192 -2.990 O3E A2D 32 A2D C2E C2*B C 0 1 N N R 15.622 9.506 7.884 8.786 -3.022 -5.153 C2E A2D 33 A2D O2E O2*B O 0 1 N N N 16.393 10.140 6.876 8.849 -4.310 -4.543 O2E A2D 34 A2D C1E C1*B C 0 1 N N R 16.496 8.650 8.767 7.432 -2.858 -5.845 C1E A2D 35 A2D N9B N9B N 0 1 Y N N 16.533 7.246 8.296 7.516 -2.209 -7.155 N9B A2D 36 A2D C8B C8B C 0 1 Y N N 15.506 6.569 7.803 7.505 -0.858 -7.389 C8B A2D 37 A2D N7B N7B N 0 1 Y N N 15.903 5.331 7.474 7.595 -0.575 -8.672 N7B A2D 38 A2D C5B C5B C 0 1 Y N N 17.197 5.226 7.775 7.668 -1.794 -9.297 C5B A2D 39 A2D C6B C6B C 0 1 Y N N 18.118 4.202 7.662 7.776 -2.157 -10.636 C6B A2D 40 A2D N6B N6B N 0 1 N N N 17.780 2.999 7.161 7.830 -1.178 -11.643 N6B A2D 41 A2D N1B N1B N 0 1 Y N N 19.370 4.419 8.069 7.829 -3.471 -10.960 N1B A2D 42 A2D C2B C2B C 0 1 Y N N 19.722 5.600 8.563 7.772 -4.369 -9.946 C2B A2D 43 A2D N3B N3B N 0 1 Y N N 18.857 6.599 8.686 7.668 -4.141 -8.619 N3B A2D 44 A2D C4B C4B C 0 1 Y N N 17.585 6.439 8.295 7.620 -2.824 -8.371 C4B A2D 45 A2D HO1A HO1A H 0 0 N N N 14.716 8.131 15.399 2.725 2.836 -0.939 HO1A A2D 46 A2D HO2B HO2B H 0 0 N N N 13.516 10.461 14.661 2.784 0.648 -1.038 HO2B A2D 47 A2D HD1 1H*A H 0 1 N N N 16.257 5.776 13.602 5.158 3.156 -4.403 HD1 A2D 48 A2D HD2 2H*A H 0 1 N N N 17.056 6.049 12.027 3.770 4.215 -4.042 HD2 A2D 49 A2D H4D H4*A H 0 1 N N N 18.652 6.457 13.737 5.237 6.214 -4.488 H4D A2D 50 A2D H3CA H3CA H 0 0 N N N 16.450 7.585 15.321 4.007 4.764 -6.519 H3CA A2D 51 A2D H3OA H3OA H 0 0 N N N 19.143 6.794 15.636 4.543 7.013 -6.430 H3OA A2D 52 A2D H2CA H2CA H 0 0 N N N 16.988 9.853 15.024 5.880 3.191 -6.751 H2CA A2D 53 A2D H2OA H2OA H 0 0 N N N 19.477 9.691 16.080 6.094 5.338 -8.578 H2OA A2D 54 A2D H1D H1*A H 0 1 N N N 19.805 9.086 14.188 7.795 5.595 -6.715 H1D A2D 55 A2D H8A H8A H 0 1 N N N 16.868 11.330 12.939 7.810 2.640 -4.396 H8A A2D 56 A2D H6A1 1H6A H 0 0 N N N 20.884 15.022 11.979 12.770 0.646 -7.428 H6A1 A2D 57 A2D H6A2 2H6A H 0 0 N N N 21.698 14.450 10.684 11.961 0.667 -5.884 H6A2 A2D 58 A2D H2A H2A H 0 1 N N N 23.401 10.976 12.790 11.172 4.409 -9.584 H2A A2D 59 A2D HE1 1H*B H 0 1 N N N 13.064 9.984 9.552 7.071 0.296 -3.863 HE1 A2D 60 A2D HE2 2H*B H 0 1 N N N 13.513 8.598 10.602 7.435 -0.315 -2.228 HE2 A2D 61 A2D H4E H4*B H 0 1 N N N 15.503 10.547 10.972 7.022 -2.644 -3.039 H4E A2D 62 A2D H3CB H3CB H 0 0 N N N 14.399 11.214 8.533 9.090 -0.977 -4.567 H3CB A2D 63 A2D H3OB H3OB H 0 0 N N N 16.820 11.488 8.014 9.521 -1.416 -2.413 H3OB A2D 64 A2D H2CB H2CB H 0 0 N N N 14.804 8.932 7.423 9.643 -2.947 -5.829 H2CB A2D 65 A2D H2OB H2OB H 0 0 N N N 15.854 10.282 6.107 9.635 -4.319 -3.969 H2OB A2D 66 A2D H1E H1*B H 0 1 N N N 17.542 8.990 8.781 6.937 -3.817 -6.032 H1E A2D 67 A2D H8B H8B H 0 1 N N N 14.504 6.955 7.684 7.429 -0.135 -6.588 H8B A2D 68 A2D H6B1 1H6B H 0 0 N N N 17.696 3.063 6.167 8.705 -0.976 -12.088 H6B1 A2D 69 A2D H6B2 2H6B H 0 0 N N N 18.487 2.331 7.393 7.015 -0.627 -11.838 H6B2 A2D 70 A2D H2B H2B H 0 1 N N N 20.745 5.753 8.875 7.816 -5.411 -10.242 H2B A2D 71 # # 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 A2D PA O5D SING N N 1 A2D PA O3A SING N N 2 A2D PA O2A DOUB N N 3 A2D PA O1A SING N N 4 A2D O1A HO1A SING N N 5 A2D O3A PB SING N N 6 A2D PB O5E SING N N 7 A2D PB O1B DOUB N N 8 A2D PB O2B SING N N 9 A2D O2B HO2B SING N N 10 A2D O5D C5D SING N N 11 A2D C5D C4D SING N N 12 A2D C5D HD1 SING N N 13 A2D C5D HD2 SING N N 14 A2D C4D O4D SING N N 15 A2D C4D C3D SING N N 16 A2D C4D H4D SING N N 17 A2D O4D C1D SING N N 18 A2D C3D C2D SING N N 19 A2D C3D O3D SING N N 20 A2D C3D H3CA SING N N 21 A2D O3D H3OA SING N N 22 A2D C2D C1D SING N N 23 A2D C2D O2D SING N N 24 A2D C2D H2CA SING N N 25 A2D O2D H2OA SING N N 26 A2D C1D N9A SING N N 27 A2D C1D H1D SING N N 28 A2D N9A C8A SING Y N 29 A2D N9A C4A SING Y N 30 A2D C8A N7A DOUB Y N 31 A2D C8A H8A SING N N 32 A2D N7A C5A SING Y N 33 A2D C5A C6A SING Y N 34 A2D C5A C4A DOUB Y N 35 A2D C6A N6A SING N N 36 A2D C6A N1A DOUB Y N 37 A2D N6A H6A1 SING N N 38 A2D N6A H6A2 SING N N 39 A2D N1A C2A SING Y N 40 A2D C2A N3A DOUB Y N 41 A2D C2A H2A SING N N 42 A2D N3A C4A SING Y N 43 A2D O5E C5E SING N N 44 A2D C5E C4E SING N N 45 A2D C5E HE1 SING N N 46 A2D C5E HE2 SING N N 47 A2D C4E C3E SING N N 48 A2D C4E O4E SING N N 49 A2D C4E H4E SING N N 50 A2D O4E C1E SING N N 51 A2D C3E C2E SING N N 52 A2D C3E O3E SING N N 53 A2D C3E H3CB SING N N 54 A2D O3E H3OB SING N N 55 A2D C2E O2E SING N N 56 A2D C2E C1E SING N N 57 A2D C2E H2CB SING N N 58 A2D O2E H2OB SING N N 59 A2D C1E N9B SING N N 60 A2D C1E H1E SING N N 61 A2D N9B C8B SING Y N 62 A2D N9B C4B SING Y N 63 A2D C8B N7B DOUB Y N 64 A2D C8B H8B SING N N 65 A2D N7B C5B SING Y N 66 A2D C5B C6B DOUB Y N 67 A2D C5B C4B SING Y N 68 A2D C6B N6B SING N N 69 A2D C6B N1B SING Y N 70 A2D N6B H6B1 SING N N 71 A2D N6B H6B2 SING N N 72 A2D N1B C2B DOUB Y N 73 A2D C2B N3B SING Y N 74 A2D C2B H2B SING N N 75 A2D N3B C4B DOUB Y N 76 # # 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 A2D SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O" A2D SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O" A2D SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O" A2D SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N" A2D SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N" A2D InChI InChI 1.03 "InChI=1S/C20H26N10O13P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(41-19)1-39-44(35,36)43-45(37,38)40-2-8-12(32)14(34)20(42-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1" A2D InChIKey InChI 1.03 AKDJDUXNKGWGAZ-XPWFQUROSA-N # # 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 A2D "SYSTEMATIC NAME" ACDLabs 10.04 "bis{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} dihydrogen diphosphate (non-preferred name)" A2D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 A2D "Create component" 2006-10-25 RCSB A2D "Modify descriptor" 2011-06-04 RCSB A2D "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A2D _pdbx_chem_comp_synonyms.name "BIS(ADENOSINE)-5'-DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##