data_45A # _chem_comp.id 45A _chem_comp.name "5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-02-09 _chem_comp.pdbx_modified_date 2019-05-07 _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 345.248 _chem_comp.one_letter_code A _chem_comp.three_letter_code 45A _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 4Y27 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 45A P P1 P 0 1 N N N 13.785 -10.798 -3.209 4.807 -0.994 -0.100 P 45A 1 45A "O4'" O1 O 0 1 N N N 10.925 -13.718 -1.935 0.596 0.236 -0.519 "O4'" 45A 2 45A "C4'" C1 C 0 1 N N R 10.802 -13.342 -3.277 1.566 1.280 -0.331 "C4'" 45A 3 45A "C3'" C2 C 0 1 N N S 9.649 -12.382 -3.292 0.912 2.361 0.552 "C3'" 45A 4 45A "C2'" C3 C 0 1 N N R 8.769 -13.052 -2.273 -0.526 1.838 0.788 "C2'" 45A 5 45A "O3'" O2 O 0 1 N N N 9.040 -12.196 -4.538 0.882 3.615 -0.132 "O3'" 45A 6 45A C6 C4 C 0 1 Y N N 9.264 -10.791 2.784 -5.014 -1.444 0.073 C6 45A 7 45A "C1'" C5 C 0 1 N N R 9.748 -13.430 -1.225 -0.707 0.844 -0.387 "C1'" 45A 8 45A C4 C6 C 0 1 Y N N 9.272 -12.324 0.922 -3.065 -0.073 -0.292 C4 45A 9 45A N3 N1 N 0 1 Y N N 8.244 -13.042 1.419 -3.862 0.842 -0.834 N3 45A 10 45A C2 C7 C 0 1 Y N N 7.849 -12.494 2.590 -5.159 0.632 -0.926 C2 45A 11 45A N1 N2 N 0 1 Y N N 8.255 -11.437 3.274 -5.731 -0.473 -0.484 N1 45A 12 45A C31 C8 C 0 1 N N N 14.318 -10.764 -4.865 5.403 -1.959 -1.527 C31 45A 13 45A OP2 O3 O 0 1 N N N 13.665 -9.504 -2.542 5.845 -0.019 0.304 OP2 45A 14 45A "O5'" O4 O 0 1 N N N 12.408 -11.531 -3.163 3.462 -0.208 -0.507 "O5'" 45A 15 45A "C5'" C9 C 0 1 N N N 12.100 -12.748 -3.834 2.808 0.717 0.363 "C5'" 45A 16 45A "O2'" O5 O 0 1 N N N 8.089 -14.101 -2.857 -1.475 2.903 0.707 "O2'" 45A 17 45A N9 N3 N 0 1 Y N N 9.996 -12.445 -0.196 -1.716 -0.166 -0.058 N9 45A 18 45A C5 C10 C 0 1 Y N N 9.817 -11.170 1.572 -3.625 -1.269 0.189 C5 45A 19 45A N7 N4 N 0 1 Y N N 10.887 -10.632 0.726 -2.608 -2.015 0.683 N7 45A 20 45A C8 C11 C 0 1 Y N N 10.870 -11.505 -0.308 -1.487 -1.370 0.539 C8 45A 21 45A N6 N5 N 0 1 N N N 9.824 -9.664 3.427 -5.623 -2.598 0.534 N6 45A 22 45A O1 O6 O 0 1 N Y N 14.843 -11.782 -2.527 4.497 -1.988 1.129 O1 45A 23 45A "H4'" H1 H 0 1 N N N 10.536 -14.217 -3.888 1.843 1.707 -1.296 "H4'" 45A 24 45A "H3'" H2 H 0 1 N N N 9.987 -11.417 -2.887 1.445 2.454 1.498 "H3'" 45A 25 45A "H2'" H3 H 0 1 N N N 8.067 -12.311 -1.864 -0.600 1.325 1.747 "H2'" 45A 26 45A H1 H4 H 0 1 N N N 8.325 -11.576 -4.452 0.481 4.332 0.378 H1 45A 27 45A "H1'" H5 H 0 1 N N N 9.388 -14.351 -0.743 -0.978 1.374 -1.300 "H1'" 45A 28 45A H2 H6 H 0 1 N N N 7.038 -13.027 3.063 -5.778 1.396 -1.372 H2 45A 29 45A H32 H7 H 0 0 N N N 15.289 -10.252 -4.928 5.612 -1.286 -2.358 H32 45A 30 45A H33 H8 H 0 0 N N N 14.422 -11.794 -5.238 6.313 -2.491 -1.251 H33 45A 31 45A H31 H9 H 0 0 N N N 13.579 -10.225 -5.477 4.638 -2.677 -1.824 H31 45A 32 45A "H5'1" H10 H 0 0 N N N 12.921 -13.464 -3.684 3.490 1.533 0.605 "H5'1" 45A 33 45A "H5'2" H11 H 0 0 N N N 11.978 -12.550 -4.909 2.511 0.207 1.280 "H5'2" 45A 34 45A "HO2'" H12 H 0 0 N N N 7.535 -14.520 -2.209 -1.345 3.597 1.367 "HO2'" 45A 35 45A H8 H13 H 0 1 N N N 11.533 -11.421 -1.156 -0.518 -1.735 0.847 H8 45A 36 45A H61 H14 H 0 1 N N N 9.323 -9.479 4.272 -6.584 -2.705 0.452 H61 45A 37 45A H62 H15 H 0 1 N N N 10.784 -9.845 3.641 -5.089 -3.299 0.938 H62 45A 38 45A H3 H16 H 0 1 N N N 15.235 -11.354 -1.775 5.265 -2.495 1.427 H3 45A 39 # # 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 45A C31 P SING N N 1 45A "O3'" "C3'" SING N N 2 45A "C5'" "C4'" SING N N 3 45A "C5'" "O5'" SING N N 4 45A "C3'" "C4'" SING N N 5 45A "C3'" "C2'" SING N N 6 45A "C4'" "O4'" SING N N 7 45A P "O5'" SING N N 8 45A P OP2 DOUB N N 9 45A "O2'" "C2'" SING N N 10 45A "C2'" "C1'" SING N N 11 45A "O4'" "C1'" SING N N 12 45A "C1'" N9 SING N N 13 45A C8 N9 SING Y N 14 45A C8 N7 DOUB Y N 15 45A N9 C4 SING Y N 16 45A N7 C5 SING Y N 17 45A C4 N3 DOUB Y N 18 45A C4 C5 SING Y N 19 45A N3 C2 SING Y N 20 45A C5 C6 DOUB Y N 21 45A C2 N1 DOUB Y N 22 45A C6 N1 SING Y N 23 45A C6 N6 SING N N 24 45A P O1 SING N N 25 45A "C4'" "H4'" SING N N 26 45A "C3'" "H3'" SING N N 27 45A "C2'" "H2'" SING N N 28 45A "O3'" H1 SING N N 29 45A "C1'" "H1'" SING N N 30 45A C2 H2 SING N N 31 45A C31 H32 SING N N 32 45A C31 H33 SING N N 33 45A C31 H31 SING N N 34 45A "C5'" "H5'1" SING N N 35 45A "C5'" "H5'2" SING N N 36 45A "O2'" "HO2'" SING N N 37 45A C8 H8 SING N N 38 45A N6 H61 SING N N 39 45A N6 H62 SING N N 40 45A O1 H3 SING N N 41 # # 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 45A SMILES ACDLabs 12.01 "O=P(O)(OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C" 45A InChI InChI 1.03 "InChI=1S/C11H16N5O6P/c1-23(19,20)21-2-5-7(17)8(18)11(22-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1" 45A InChIKey InChI 1.03 PXSSQXBLDTZHLF-IOSLPCCCSA-N 45A SMILES_CANONICAL CACTVS 3.385 "C[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 45A SMILES CACTVS 3.385 "C[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 45A SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 45A SMILES "OpenEye OEToolkits" 1.9.2 "CP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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 45A "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine" 45A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-methyl-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 45A "Create component" 2015-02-09 EBI 45A "Initial release" 2015-11-18 RCSB 45A "Other modification" 2019-05-07 EBI ##