data_3DA # _chem_comp.id 3DA _chem_comp.name "3'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-02-09 _chem_comp.pdbx_modified_date 2011-06-04 _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 331.222 _chem_comp.one_letter_code A _chem_comp.three_letter_code 3DA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1S77 _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 3DA P P P 0 1 N N N -38.973 10.018 44.822 3.453 -3.257 2.109 P 3DA 1 3DA O1P O1P O 0 1 N N N -39.123 8.804 45.670 4.812 -3.892 2.158 O1P 3DA 2 3DA O2P O2P O 0 1 N N N -39.319 9.947 43.381 2.207 -4.282 2.212 O2P 3DA 3 3DA "O5'" O5* O 0 1 N N N -39.847 11.170 45.479 3.142 -2.407 0.767 "O5'" 3DA 4 3DA "C5'" C5* C 0 1 N N N -41.165 11.430 45.018 1.877 -1.776 0.645 "C5'" 3DA 5 3DA "C4'" C4* C 0 1 N N S -41.388 12.915 44.925 1.818 -1.044 -0.687 "C4'" 3DA 6 3DA "O4'" O4* O 0 1 N N N -40.229 13.524 44.297 1.970 -2.005 -1.750 "O4'" 3DA 7 3DA "C1'" C1* C 0 1 N N R -40.648 14.579 43.455 0.760 -2.026 -2.527 "C1'" 3DA 8 3DA N9 N9 N 0 1 Y N N -40.321 14.192 42.079 0.455 -3.399 -2.922 N9 3DA 9 3DA C4 C4 C 0 1 Y N N -40.504 14.968 40.962 -0.144 -3.804 -4.080 C4 3DA 10 3DA N3 N3 N 0 1 Y N N -40.979 16.224 40.918 -0.577 -3.035 -5.090 N3 3DA 11 3DA C2 C2 C 0 1 Y N N -41.031 16.659 39.659 -1.117 -3.797 -6.066 C2 3DA 12 3DA N1 N1 N 0 1 Y N N -40.691 16.023 38.531 -1.250 -5.145 -6.116 N1 3DA 13 3DA C6 C6 C 0 1 Y N N -40.224 14.759 38.616 -0.791 -5.859 -5.060 C6 3DA 14 3DA N6 N6 N 0 1 N N N -39.905 14.126 37.492 -0.900 -7.260 -5.053 N6 3DA 15 3DA C5 C5 C 0 1 Y N N -40.111 14.187 39.890 -0.212 -5.185 -3.989 C5 3DA 16 3DA N7 N7 N 0 1 Y N N -39.671 12.941 40.322 0.331 -5.622 -2.807 N7 3DA 17 3DA C8 C8 C 0 1 Y N N -39.808 12.995 41.626 0.722 -4.526 -2.190 C8 3DA 18 3DA "C2'" C2* C 0 1 N N R -42.160 14.763 43.684 -0.316 -1.374 -1.672 "C2'" 3DA 19 3DA "O2'" O2* O 0 1 N N N -42.417 15.692 44.715 -1.318 -0.781 -2.473 "O2'" 3DA 20 3DA "C3'" C3* C 0 1 N N N -42.581 13.358 44.097 0.489 -0.340 -0.918 "C3'" 3DA 21 3DA O3P O3P O 0 1 N Y N ? ? ? 3.155 -2.190 3.287 O3P 3DA 22 3DA HOP2 2HOP H 0 0 N N N -39.223 10.721 42.839 2.206 -4.958 2.923 HOP2 3DA 23 3DA "H5'1" 1H5* H 0 0 N N N -41.382 10.912 44.054 1.095 -2.538 0.697 "H5'1" 3DA 24 3DA "H5'2" 2H5* H 0 0 N N N -41.936 10.928 45.648 1.751 -1.073 1.473 "H5'2" 3DA 25 3DA "H4'" H4* H 0 1 N N N -41.572 13.232 45.977 2.650 -0.335 -0.739 "H4'" 3DA 26 3DA "H1'" H1* H 0 1 N N N -40.143 15.550 43.666 0.934 -1.487 -3.465 "H1'" 3DA 27 3DA H2 H2 H 0 1 N N N -41.407 17.688 39.533 -1.495 -3.258 -6.928 H2 3DA 28 3DA HN61 1HN6 H 0 0 N N N -39.552 13.171 37.556 -1.332 -7.716 -4.273 HN61 3DA 29 3DA HN62 2HN6 H 0 0 N N N -39.236 14.692 36.970 -0.462 -7.792 -5.781 HN62 3DA 30 3DA H8 H8 H 0 1 N N N -39.526 12.139 42.262 1.200 -4.486 -1.221 H8 3DA 31 3DA "H2'1" 1H2* H 0 0 N N N -42.704 15.161 42.796 -0.780 -2.089 -0.983 "H2'1" 3DA 32 3DA "HO'2" 2HO* H 0 0 N N N -43.349 15.805 44.856 -1.354 -1.294 -3.296 "HO'2" 3DA 33 3DA "H3'1" 1H3* H 0 0 N N N -42.856 12.677 43.257 0.635 0.549 -1.545 "H3'1" 3DA 34 3DA "H3'2" 2H3* H 0 0 N N N -43.568 13.289 44.610 0.002 -0.002 0.002 "H3'2" 3DA 35 3DA HOP3 3HOP H 0 0 N N N 0.095 0.774 -0.541 3.360 -2.437 4.214 HOP3 3DA 36 # 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 3DA P O1P DOUB N N 1 3DA P O2P SING N N 2 3DA P "O5'" SING N N 3 3DA P O3P SING N N 4 3DA O2P HOP2 SING N N 5 3DA "O5'" "C5'" SING N N 6 3DA "C5'" "C4'" SING N N 7 3DA "C5'" "H5'1" SING N N 8 3DA "C5'" "H5'2" SING N N 9 3DA "C4'" "O4'" SING N N 10 3DA "C4'" "C3'" SING N N 11 3DA "C4'" "H4'" SING N N 12 3DA "O4'" "C1'" SING N N 13 3DA "C1'" N9 SING N N 14 3DA "C1'" "C2'" SING N N 15 3DA "C1'" "H1'" SING N N 16 3DA N9 C4 SING Y N 17 3DA N9 C8 SING Y N 18 3DA C4 N3 SING Y N 19 3DA C4 C5 DOUB Y N 20 3DA N3 C2 DOUB Y N 21 3DA C2 N1 SING Y N 22 3DA C2 H2 SING N N 23 3DA N1 C6 DOUB Y N 24 3DA C6 N6 SING N N 25 3DA C6 C5 SING Y N 26 3DA N6 HN61 SING N N 27 3DA N6 HN62 SING N N 28 3DA C5 N7 SING Y N 29 3DA N7 C8 DOUB Y N 30 3DA C8 H8 SING N N 31 3DA "C2'" "O2'" SING N N 32 3DA "C2'" "C3'" SING N N 33 3DA "C2'" "H2'1" SING N N 34 3DA "O2'" "HO'2" SING N N 35 3DA "C3'" "H3'1" SING N N 36 3DA "C3'" "H3'2" SING N N 37 3DA O3P HOP3 SING N N 38 # 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 3DA SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3" 3DA SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)C[C@H]3O" 3DA SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)C[CH]3O" 3DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H](C[C@H](O3)COP(=O)(O)O)O)N" 3DA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(CC(O3)COP(=O)(O)O)O)N" 3DA InChI InChI 1.03 "InChI=1S/C10H14N5O6P/c11-8-7-9(13-3-12-8)15(4-14-7)10-6(16)1-5(21-10)2-20-22(17,18)19/h3-6,10,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,10+/m0/s1" 3DA InChIKey InChI 1.03 XKFCKNDXVMFENB-BAJZRUMYSA-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 3DA "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-deoxy-5'-adenylic acid ; 3DA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-oxolan-2-yl]methyl 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 3DA "Create component" 2004-02-09 RCSB 3DA "Modify linking type" 2011-06-04 RCSB 3DA "Modify descriptor" 2011-06-04 RCSB #