data_A3P # _chem_comp.id A3P _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _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 427.201 _chem_comp.one_letter_code A _chem_comp.three_letter_code A3P _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 1AQU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A3P P1 P1 P 0 1 N N N N N N 4.090 23.888 22.033 3.047 -0.319 -2.419 P1 A3P 1 A3P O1P O1P O 0 1 N N N N N N 4.339 24.834 23.134 2.080 -0.681 -3.479 O1P A3P 2 A3P O2P O2P O 0 1 N N N N N N 2.805 23.167 22.209 4.314 0.422 -3.080 O2P A3P 3 A3P O3P O3P O 0 1 N Y N N N N 4.134 24.595 20.729 3.540 -1.653 -1.664 O3P A3P 4 A3P P2 P2 P 0 1 N N N N N N 10.492 20.644 24.788 -2.728 0.073 -3.807 P2 A3P 5 A3P O4P O4P O 0 1 N N N N N N 10.264 19.264 25.205 -2.932 -1.369 -3.549 O4P A3P 6 A3P O5P O5P O 0 1 N N N N N N 11.781 20.754 24.048 -4.149 0.773 -4.096 O5P A3P 7 A3P O6P O6P O 0 1 N N N N N N 10.471 21.568 25.947 -1.768 0.259 -5.086 O6P A3P 8 A3P "O5'" O5* O 0 1 N N N N N N 9.298 21.064 23.779 -2.045 0.758 -2.520 "O5'" A3P 9 A3P "C5'" C5* C 0 1 N N N N N N 7.941 21.288 24.183 -0.794 0.097 -2.316 "C5'" A3P 10 A3P "C4'" C4* C 0 1 N N R N N N 7.078 21.449 22.912 -0.090 0.703 -1.100 "C4'" A3P 11 A3P "O4'" O4* O 0 1 N N N N N N 6.948 20.124 22.293 -0.888 0.516 0.088 "O4'" A3P 12 A3P "C3'" C3* C 0 1 N N S N N N 5.639 21.942 23.164 1.229 -0.045 -0.812 "C3'" A3P 13 A3P "O3'" O3* O 0 1 N N N N N N 5.251 22.785 22.043 2.340 0.666 -1.361 "O3'" A3P 14 A3P "C2'" C2* C 0 1 N N R N N N 4.889 20.606 23.288 1.314 -0.077 0.732 "C2'" A3P 15 A3P "O2'" O2* O 0 1 N N N N N N 3.481 20.642 23.168 2.481 0.612 1.183 "O2'" A3P 16 A3P "C1'" C1* C 0 1 N N R N N N 5.564 19.791 22.177 0.033 0.654 1.191 "C1'" A3P 17 A3P N9 N9 N 0 1 Y N N N N N 5.352 18.337 22.289 -0.512 0.021 2.394 N9 A3P 18 A3P C8 C8 C 0 1 Y N N N N N 5.639 17.490 23.342 -1.396 -1.015 2.429 C8 A3P 19 A3P N7 N7 N 0 1 Y N N N N N 5.325 16.226 23.132 -1.667 -1.326 3.663 N7 A3P 20 A3P C5 C5 C 0 1 Y N N N N N 4.791 16.227 21.850 -0.972 -0.515 4.496 C5 A3P 21 A3P C6 C6 C 0 1 Y N N N N N 4.257 15.187 21.019 -0.873 -0.382 5.891 C6 A3P 22 A3P N6 N6 N 0 1 N N N N N N 4.182 13.908 21.396 -1.588 -1.215 6.734 N6 A3P 23 A3P N1 N1 N 0 1 Y N N N N N 3.801 15.535 19.768 -0.072 0.558 6.383 N1 A3P 24 A3P C2 C2 C 0 1 Y N N N N N 3.870 16.831 19.368 0.612 1.357 5.586 C2 A3P 25 A3P N3 N3 N 0 1 Y N N N N N 4.350 17.901 20.061 0.547 1.273 4.274 N3 A3P 26 A3P C4 C4 C 0 1 Y N N N N N 4.798 17.526 21.301 -0.226 0.362 3.691 C4 A3P 27 A3P HOP2 2HOP H 0 0 N N N N N N 2.644 22.556 21.498 4.708 -0.200 -3.705 HOP2 A3P 28 A3P HOP3 3HOP H 0 0 N N N N N N 3.973 23.984 20.018 4.167 -1.373 -0.983 HOP3 A3P 29 A3P HOP5 5HOP H 0 0 N N N N N N 11.929 21.652 23.776 -4.523 0.335 -4.873 HOP5 A3P 30 A3P HOP6 6HOP H 0 0 N N N N N N 10.619 22.466 25.675 -1.661 1.211 -5.220 HOP6 A3P 31 A3P "H5'1" 1H5* H 0 0 N N N N N N 7.558 20.492 24.863 -0.168 0.223 -3.199 "H5'1" A3P 32 A3P "H5'2" 2H5* H 0 0 N N N N N N 7.838 22.148 24.884 -0.968 -0.964 -2.143 "H5'2" A3P 33 A3P "H4'" H4* H 0 1 N N N N N N 7.593 22.212 22.284 0.103 1.763 -1.265 "H4'" A3P 34 A3P "H3'" H3* H 0 1 N N N N N N 5.451 22.581 24.058 1.189 -1.058 -1.214 "H3'" A3P 35 A3P "H2'" H2* H 0 1 N N N N N N 4.967 20.185 24.317 1.315 -1.105 1.093 "H2'" A3P 36 A3P "HO2'" *HO2 H 0 0 N N N N N N 3.017 19.816 23.244 2.481 0.560 2.149 "HO2'" A3P 37 A3P "H1'" H1* H 0 1 N N N N N N 5.128 20.042 21.181 0.244 1.707 1.379 "H1'" A3P 38 A3P H8 H8 H 0 1 N N N N N N 6.093 17.805 24.296 -1.811 -1.505 1.561 H8 A3P 39 A3P HN61 1HN6 H 0 0 N N N N N N 3.802 13.168 20.805 -1.508 -1.116 7.696 HN61 A3P 40 A3P HN62 2HN6 H 0 0 N N N N N N 3.670 13.882 22.278 -2.171 -1.895 6.364 HN62 A3P 41 A3P H2 H2 H 0 1 N N N N N N 3.488 17.040 18.354 1.251 2.108 6.027 H2 A3P 42 # 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 A3P P1 O1P DOUB N N 1 A3P P1 O2P SING N N 2 A3P P1 O3P SING N N 3 A3P P1 "O3'" SING N N 4 A3P O2P HOP2 SING N N 5 A3P O3P HOP3 SING N N 6 A3P P2 O4P DOUB N N 7 A3P P2 O5P SING N N 8 A3P P2 O6P SING N N 9 A3P P2 "O5'" SING N N 10 A3P O5P HOP5 SING N N 11 A3P O6P HOP6 SING N N 12 A3P "O5'" "C5'" SING N N 13 A3P "C5'" "C4'" SING N N 14 A3P "C5'" "H5'1" SING N N 15 A3P "C5'" "H5'2" SING N N 16 A3P "C4'" "O4'" SING N N 17 A3P "C4'" "C3'" SING N N 18 A3P "C4'" "H4'" SING N N 19 A3P "O4'" "C1'" SING N N 20 A3P "C3'" "O3'" SING N N 21 A3P "C3'" "C2'" SING N N 22 A3P "C3'" "H3'" SING N N 23 A3P "C2'" "O2'" SING N N 24 A3P "C2'" "C1'" SING N N 25 A3P "C2'" "H2'" SING N N 26 A3P "O2'" "HO2'" SING N N 27 A3P "C1'" N9 SING N N 28 A3P "C1'" "H1'" SING N N 29 A3P N9 C8 SING Y N 30 A3P N9 C4 SING Y N 31 A3P C8 N7 DOUB Y N 32 A3P C8 H8 SING N N 33 A3P N7 C5 SING Y N 34 A3P C5 C6 SING Y N 35 A3P C5 C4 DOUB Y N 36 A3P C6 N6 SING N N 37 A3P C6 N1 DOUB Y N 38 A3P N6 HN61 SING N N 39 A3P N6 HN62 SING N N 40 A3P N1 C2 SING Y N 41 A3P C2 N3 DOUB Y N 42 A3P C2 H2 SING N N 43 A3P N3 C4 SING Y 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 A3P SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O" A3P SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O" A3P SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O" A3P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)OP(=O)(O)O)O)N" A3P SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)OP(=O)(O)O)O)N" A3P InChI InChI 1.03 "InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1" A3P InChIKey InChI 1.03 WHTCPDAXWFLDIH-KQYNXXCUSA-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 A3P "SYSTEMATIC NAME" ACDLabs 10.04 ;adenosine 3',5'-bis(dihydrogen phosphate) ; A3P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(phosphonooxymethyl)oxolan-3-yl] 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 A3P "Create component" 1999-07-08 RCSB A3P "Modify descriptor" 2011-06-04 RCSB A3P "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A3P _pdbx_chem_comp_pcm.modified_residue_id TYR _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom P1 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OH _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #