data_2DA # _chem_comp.id 2DA _chem_comp.name "2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O5 P" _chem_comp.mon_nstd_parent_comp_id DA _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 315.222 _chem_comp.one_letter_code A _chem_comp.three_letter_code 2DA _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 1QSY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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 2DA P P P 0 1 N N N N N N 0.327 28.898 -5.722 0.644 -0.205 -4.721 P 2DA 1 2DA OP1 O1P O 0 1 N N N N N N 0.447 27.871 -6.787 1.689 0.774 -4.350 OP1 2DA 2 2DA OP2 O2P O 0 1 N N N N N N 0.818 28.593 -4.355 1.327 -1.470 -5.446 OP2 2DA 3 2DA OP3 O3P O 0 1 N Y N N N N 1.077 30.250 -6.175 -0.407 0.485 -5.725 OP3 2DA 4 2DA "O5'" O5* O 0 1 N N N N N N -1.210 29.310 -5.632 -0.124 -0.697 -3.395 "O5'" 2DA 5 2DA "C5'" C5* C 0 1 N N N N N N -1.700 30.155 -4.602 -0.706 0.463 -2.800 "C5'" 2DA 6 2DA "C4'" C4* C 0 1 N N S N N N -3.206 30.192 -4.637 -1.456 0.063 -1.527 "C4'" 2DA 7 2DA "O4'" O4* O 0 1 N N N N N N -3.643 30.877 -5.839 -0.537 -0.425 -0.523 "O4'" 2DA 8 2DA "C3'" C3* C 0 1 N N N N N N -3.893 28.839 -4.692 -2.099 1.304 -0.859 "C3'" 2DA 9 2DA "C2'" C2* C 0 1 N N N N N N -5.232 29.191 -5.329 -2.221 0.852 0.616 "C2'" 2DA 10 2DA "C1'" C1* C 0 1 N N R N N N -4.823 30.272 -6.330 -1.198 -0.292 0.746 "C1'" 2DA 11 2DA N9 N9 N 0 1 Y N N N N N -4.537 29.758 -7.669 -0.218 0.030 1.785 N9 2DA 12 2DA C8 C8 C 0 1 Y N N N N N -3.324 29.362 -8.182 0.956 0.698 1.607 C8 2DA 13 2DA N7 N7 N 0 1 Y N N N N N -3.381 28.972 -9.432 1.580 0.811 2.743 N7 2DA 14 2DA C5 C5 C 0 1 Y N N N N N -4.723 29.117 -9.765 0.845 0.230 3.721 C5 2DA 15 2DA C6 C6 C 0 1 Y N N N N N -5.438 28.881 -10.959 1.013 0.041 5.104 C6 2DA 16 2DA N6 N6 N 0 1 N N N N N N -4.879 28.428 -12.080 2.138 0.519 5.752 N6 2DA 17 2DA N1 N1 N 0 1 Y N N N N N -6.766 29.130 -10.955 0.063 -0.602 5.775 N1 2DA 18 2DA C2 C2 C 0 1 Y N N N N N -7.331 29.585 -9.824 -1.013 -1.061 5.164 C2 2DA 19 2DA N3 N3 N 0 1 Y N N N N N -6.768 29.846 -8.646 -1.210 -0.913 3.871 N3 2DA 20 2DA C4 C4 C 0 1 Y N N N N N -5.448 29.590 -8.685 -0.314 -0.283 3.118 C4 2DA 21 2DA HOP2 2HOP H 0 0 N N N N N N 0.741 29.250 -3.673 1.776 -1.132 -6.233 HOP2 2DA 22 2DA HOP3 3HOP H 0 0 N N N N N N 1.000 30.907 -5.493 -1.069 -0.185 -5.942 HOP3 2DA 23 2DA "H5'" 1H5* H 0 1 N N N N N N -1.312 29.858 -3.599 -1.402 0.921 -3.502 "H5'" 2DA 24 2DA "H5''" 2H5* H 0 0 N N N N N N -1.255 31.176 -4.653 0.079 1.176 -2.549 "H5''" 2DA 25 2DA "H4'" H4* H 0 1 N N N N N N -3.485 30.695 -3.682 -2.213 -0.688 -1.750 "H4'" 2DA 26 2DA "H3'1" 1H3* H 0 0 N N N N N N -3.318 28.037 -5.212 -3.080 1.511 -1.285 "H3'1" 2DA 27 2DA "H3'2" 2H3* H 0 0 N N N N N N -3.960 28.302 -3.716 -1.447 2.174 -0.946 "H3'2" 2DA 28 2DA "H2'" 1H2* H 0 1 N N N N N N -5.792 28.330 -5.762 -3.228 0.489 0.821 "H2'" 2DA 29 2DA "H2''" 2H2* H 0 0 N N N N N N -6.035 29.485 -4.613 -1.965 1.671 1.288 "H2''" 2DA 30 2DA "H1'" H1* H 0 1 N N N N N N -5.679 30.979 -6.426 -1.711 -1.221 0.996 "H1'" 2DA 31 2DA H8 H8 H 0 1 N N N N N N -2.370 29.357 -7.628 1.316 1.078 0.662 H8 2DA 32 2DA HN61 1HN6 H 0 0 N N N N N N -5.395 28.257 -12.942 2.240 0.386 6.708 HN61 2DA 33 2DA HN62 2HN6 H 0 0 N N N N N N -4.392 27.562 -11.844 2.826 0.984 5.251 HN62 2DA 34 2DA H2 H2 H 0 1 N N N N N N -8.417 29.771 -9.869 -1.760 -1.579 5.747 H2 2DA 35 # 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 2DA P OP1 DOUB N N 1 2DA P OP2 SING N N 2 2DA P OP3 SING N N 3 2DA P "O5'" SING N N 4 2DA OP2 HOP2 SING N N 5 2DA OP3 HOP3 SING N N 6 2DA "O5'" "C5'" SING N N 7 2DA "C5'" "C4'" SING N N 8 2DA "C5'" "H5'" SING N N 9 2DA "C5'" "H5''" SING N N 10 2DA "C4'" "O4'" SING N N 11 2DA "C4'" "C3'" SING N N 12 2DA "C4'" "H4'" SING N N 13 2DA "O4'" "C1'" SING N N 14 2DA "C3'" "C2'" SING N N 15 2DA "C3'" "H3'1" SING N N 16 2DA "C3'" "H3'2" SING N N 17 2DA "C2'" "C1'" SING N N 18 2DA "C2'" "H2'" SING N N 19 2DA "C2'" "H2''" SING N N 20 2DA "C1'" N9 SING N N 21 2DA "C1'" "H1'" SING N N 22 2DA N9 C8 SING Y N 23 2DA N9 C4 SING Y N 24 2DA C8 N7 DOUB Y N 25 2DA C8 H8 SING N N 26 2DA N7 C5 SING Y N 27 2DA C5 C6 SING Y N 28 2DA C5 C4 DOUB Y N 29 2DA C6 N6 SING N N 30 2DA C6 N1 DOUB Y N 31 2DA N6 HN61 SING N N 32 2DA N6 HN62 SING N N 33 2DA N1 C2 SING Y N 34 2DA C2 N3 DOUB Y N 35 2DA C2 H2 SING N N 36 2DA N3 C4 SING Y N 37 # 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 2DA SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3" 2DA SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3CC[C@@H](CO[P](O)(O)=O)O3" 2DA SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3CC[CH](CO[P](O)(O)=O)O3" 2DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)COP(=O)(O)O)N" 2DA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CCC(O3)COP(=O)(O)O)N" 2DA InChI InChI 1.03 "InChI=1S/C10H14N5O5P/c11-9-8-10(13-4-12-9)15(5-14-8)7-2-1-6(20-7)3-19-21(16,17)18/h4-7H,1-3H2,(H2,11,12,13)(H2,16,17,18)/t6-,7+/m0/s1" 2DA InChIKey InChI 1.03 PUSXDQXVJDGIBK-NKWVEPMBSA-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 2DA "SYSTEMATIC NAME" ACDLabs 10.04 "[(2S,5R)-5-(6-amino-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate" 2DA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(6-aminopurin-9-yl)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 2DA "Create component" 1999-07-08 EBI 2DA "Modify descriptor" 2011-06-04 RCSB 2DA "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 2DA _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 P _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 ? #