data_DA # _chem_comp.id DA _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-01-25 _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 331.222 _chem_comp.one_letter_code A _chem_comp.three_letter_code DA _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 _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 DA OP3 O3P O 0 1 N Y N N N N -5.588 6.537 9.160 1.845 -1.282 -5.339 OP3 DA 1 DA P P P 0 1 N N N N N N -5.219 8.126 9.083 0.934 -0.156 -4.636 P DA 2 DA OP1 O1P O 0 1 N N N N N N -5.953 8.789 10.199 1.781 0.996 -4.255 OP1 DA 3 DA OP2 O2P O 0 1 N N N N N N -5.398 8.539 7.715 -0.204 0.331 -5.665 OP2 DA 4 DA "O5'" O5* O 0 1 N N N N N N -3.672 8.039 9.404 0.241 -0.771 -3.320 "O5'" DA 5 DA "C5'" C5* C 0 1 N N N N N N -3.254 7.714 10.749 -0.549 0.270 -2.744 "C5'" DA 6 DA "C4'" C4* C 0 1 N N R N N N -1.972 6.935 10.652 -1.239 -0.251 -1.482 "C4'" DA 7 DA "O4'" O4* O 0 1 N N N N N N -2.205 5.629 10.096 -0.267 -0.564 -0.458 "O4'" DA 8 DA "C3'" C3* C 0 1 N N S N N N -0.884 7.550 9.774 -2.105 0.859 -0.835 "C3'" DA 9 DA "O3'" O3* O 0 1 N N N N N N 0.377 7.277 10.436 -3.409 0.895 -1.418 "O3'" DA 10 DA "C2'" C2* C 0 1 N N N N N N -1.011 6.815 8.448 -2.173 0.398 0.640 "C2'" DA 11 DA "C1'" C1* C 0 1 N N R N N N -1.499 5.434 8.851 -0.965 -0.545 0.797 "C1'" DA 12 DA N9 N9 N 0 1 Y N N N N N -2.414 4.796 7.924 -0.078 -0.047 1.852 N9 DA 13 DA C8 C8 C 0 1 Y N N N N N -3.356 5.385 7.125 0.962 0.817 1.689 C8 DA 14 DA N7 N7 N 0 1 Y N N N N N -4.176 4.542 6.586 1.535 1.044 2.835 N7 DA 15 DA C5 C5 C 0 1 Y N N N N N -3.788 3.302 7.070 0.897 0.346 3.805 C5 DA 16 DA C6 C6 C 0 1 Y N N N N N -4.288 1.998 6.885 1.069 0.196 5.191 C6 DA 17 DA N6 N6 N 0 1 N N N N N N -5.369 1.727 6.154 2.079 0.869 5.856 N6 DA 18 DA N1 N1 N 0 1 Y N N N N N -3.627 0.989 7.493 0.236 -0.603 5.850 N1 DA 19 DA C2 C2 C 0 1 Y N N N N N -2.553 1.276 8.249 -0.729 -1.249 5.224 C2 DA 20 DA N3 N3 N 0 1 Y N N N N N -2.016 2.460 8.510 -0.925 -1.144 3.927 N3 DA 21 DA C4 C4 C 0 1 Y N N N N N -2.678 3.447 7.892 -0.142 -0.368 3.184 C4 DA 22 DA HOP3 3HOP H 0 0 N N N N N N -5.120 6.114 8.449 2.241 -0.873 -6.121 HOP3 DA 23 DA HOP2 2HOP H 0 0 N N N N N N -4.930 8.116 7.004 -0.732 -0.447 -5.887 HOP2 DA 24 DA "H5'" 1H5* H 0 1 N N N N N N -3.167 8.611 11.405 -1.302 0.594 -3.463 "H5'" DA 25 DA "H5''" 2H5* H 0 0 N N N N N N -4.041 7.181 11.331 0.092 1.112 -2.486 "H5''" DA 26 DA "H4'" H4* H 0 1 N N N N N N -1.615 6.919 11.708 -1.846 -1.126 -1.712 "H4'" DA 27 DA "H3'" H3* H 0 1 N N N N N N -0.959 8.650 9.610 -1.617 1.830 -0.918 "H3'" DA 28 DA "HO3'" H3T H 0 0 N Y N N N N 1.053 7.659 9.889 -3.924 1.538 -0.913 "HO3'" DA 29 DA "H2'" 1H2* H 0 1 N N N N N N -1.652 7.329 7.695 -3.103 -0.136 0.831 "H2'" DA 30 DA "H2''" 2H2* H 0 0 N N N N N N -0.082 6.814 7.830 -2.079 1.253 1.311 "H2''" DA 31 DA "H1'" H1* H 0 1 N N N N N N -0.610 4.761 8.898 -1.309 -1.549 1.046 "H1'" DA 32 DA H8 H8 H 0 1 N N N N N N -3.448 6.466 6.928 1.266 1.250 0.748 H8 DA 33 DA H61 1H6 H 0 1 N N N N N N -5.731 0.782 6.020 2.185 0.761 6.814 H61 DA 34 DA H62 2H6 H 0 1 N N N N N N -5.218 2.128 5.228 2.683 1.447 5.363 H62 DA 35 DA H2 H2 H 0 1 N N N N N N -2.040 0.420 8.721 -1.383 -1.889 5.798 H2 DA 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 DA OP3 P SING N N 1 DA OP3 HOP3 SING N N 2 DA P OP1 DOUB N N 3 DA P OP2 SING N N 4 DA P "O5'" SING N N 5 DA OP2 HOP2 SING N N 6 DA "O5'" "C5'" SING N N 7 DA "C5'" "C4'" SING N N 8 DA "C5'" "H5'" SING N N 9 DA "C5'" "H5''" SING N N 10 DA "C4'" "O4'" SING N N 11 DA "C4'" "C3'" SING N N 12 DA "C4'" "H4'" SING N N 13 DA "O4'" "C1'" SING N N 14 DA "C3'" "O3'" SING N N 15 DA "C3'" "C2'" SING N N 16 DA "C3'" "H3'" SING N N 17 DA "O3'" "HO3'" SING N N 18 DA "C2'" "C1'" SING N N 19 DA "C2'" "H2'" SING N N 20 DA "C2'" "H2''" SING N N 21 DA "C1'" N9 SING N N 22 DA "C1'" "H1'" SING N N 23 DA N9 C8 SING Y N 24 DA N9 C4 SING Y N 25 DA C8 N7 DOUB Y N 26 DA C8 H8 SING N N 27 DA N7 C5 SING Y N 28 DA C5 C6 SING Y N 29 DA C5 C4 DOUB Y N 30 DA C6 N6 SING N N 31 DA C6 N1 DOUB Y N 32 DA N6 H61 SING N N 33 DA N6 H62 SING N N 34 DA N1 C2 SING Y N 35 DA C2 N3 DOUB Y N 36 DA C2 H2 SING N N 37 DA N3 C4 SING Y 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 DA SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O" DA SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" DA SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N" DA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N" DA InChI InChI 1.03 "InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1" DA InChIKey InChI 1.03 KHWCHTKSEGGWEX-RRKCRQDMSA-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 DA "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-adenylic acid ; DA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-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 DA "Create component" 2001-01-25 RCSB DA "Modify descriptor" 2011-06-04 RCSB DA "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 DA PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O1P ? ? 2 DA PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O3P ? ? 3 DA PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "O3'" P ? ? 4 DA SER None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OG ? ? 5 DA TYR None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OH ? ? #