data_A38 # _chem_comp.id A38 _chem_comp.name ;8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1996-06-10 _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 347.221 _chem_comp.one_letter_code A _chem_comp.three_letter_code A38 _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 Y _chem_comp.pdbx_model_coordinates_db_code 1FJB _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 A38 O3P O3P O 0 1 N Y N 11.030 2.072 -4.871 -4.207 -1.737 -1.073 O3P A38 1 A38 P P P 0 1 N N N 10.518 3.166 -4.014 -4.606 -1.068 0.186 P A38 2 A38 O1P O1P O 0 1 N N N 11.401 3.770 -2.991 -5.198 -2.160 1.210 O1P A38 3 A38 O2P O2P O 0 1 N N N 9.965 4.352 -4.959 -5.732 0.039 -0.129 O2P A38 4 A38 "O5'" O5* O 0 1 N N N 9.191 2.630 -3.283 -3.321 -0.355 0.845 "O5'" A38 5 A38 "C5'" C5* C 0 1 N N N 8.563 3.376 -2.231 -2.774 0.512 -0.151 "C5'" A38 6 A38 "C4'" C4* C 0 1 N N R 7.317 2.681 -1.707 -1.544 1.225 0.414 "C4'" A38 7 A38 "O4'" O4* O 0 1 N N N 6.282 2.581 -2.700 -0.443 0.300 0.572 "O4'" A38 8 A38 "C3'" C3* C 0 1 N N S 7.612 1.290 -1.176 -1.002 2.265 -0.600 "C3'" A38 9 A38 "O3'" O3* O 0 1 N N N 6.786 1.125 -0.015 -1.675 3.517 -0.455 "O3'" A38 10 A38 "C2'" C2* C 0 1 N N N 7.082 0.445 -2.427 0.483 2.384 -0.180 "C2'" A38 11 A38 "C1'" C1* C 0 1 N N R 5.740 1.265 -2.607 0.760 1.085 0.602 "C1'" A38 12 A38 N9 N9 N 0 1 N N N 4.989 1.023 -3.866 1.853 0.345 -0.034 N9 A38 13 A38 C8 C8 C 0 1 N N N 5.595 0.720 -5.074 1.823 -0.197 -1.266 C8 A38 14 A38 N7 N7 N 0 1 N N N 4.601 0.606 -5.963 3.000 -0.801 -1.523 N7 A38 15 A38 C5 C5 C 0 1 Y N N 3.358 0.811 -5.446 3.823 -0.634 -0.412 C5 A38 16 A38 C6 C6 C 0 1 Y N N 2.031 0.815 -5.899 5.118 -1.032 -0.086 C6 A38 17 A38 N6 N6 N 0 1 N N N 1.662 0.578 -7.153 5.885 -1.756 -0.988 N6 A38 18 A38 N1 N1 N 0 1 Y N N 1.090 1.079 -4.987 5.607 -0.697 1.106 N1 A38 19 A38 C2 C2 C 0 1 Y N N 1.442 1.319 -3.728 4.883 -0.009 1.967 C2 A38 20 A38 N3 N3 N 0 1 Y N N 2.654 1.342 -3.187 3.652 0.380 1.699 N3 A38 21 A38 C4 C4 C 0 1 Y N N 3.598 1.075 -4.113 3.089 0.088 0.532 C4 A38 22 A38 O O O 0 1 N N N 6.788 0.578 -5.326 0.877 -0.150 -2.030 O A38 23 A38 H3P H3P H 0 1 N N N 10.269 1.574 -5.261 ? ? ? H3P A38 24 A38 H2P H2P H 0 1 N N N 8.975 4.345 -4.953 -5.963 0.450 0.716 H2P A38 25 A38 "H5'1" 1H5* H 0 0 N N N 9.278 3.495 -1.404 -3.521 1.251 -0.440 "H5'1" A38 26 A38 "H5'2" 2H5* H 0 0 N N N 8.262 4.352 -2.639 -2.486 -0.073 -1.024 "H5'2" A38 27 A38 "H4'" H4* H 0 1 N N N 6.963 3.317 -0.882 -1.781 1.703 1.364 "H4'" A38 28 A38 "H3'" H3* H 0 1 N N N 8.639 1.035 -0.876 -1.089 1.894 -1.621 "H3'" A38 29 A38 HA HA H 0 1 N N N 6.658 0.160 0.165 -1.232 4.142 -1.045 HA A38 30 A38 "H2'1" 1H2* H 0 0 N N N 7.746 0.515 -3.302 0.629 3.254 0.461 "H2'1" A38 31 A38 "H2'2" 2H2* H 0 0 N N N 6.997 -0.645 -2.303 1.125 2.445 -1.059 "H2'2" A38 32 A38 "H1'" H1* H 0 1 N N N 5.020 1.024 -1.811 1.023 1.322 1.633 "H1'" A38 33 A38 H7 H7 H 0 1 N N N 4.757 0.390 -6.922 3.235 -1.267 -2.340 H7 A38 34 A38 H6N1 1H6N H 0 0 N N N 2.349 0.380 -7.845 6.787 -2.024 -0.753 H6N1 A38 35 A38 H6N2 2H6N H 0 0 N N N 0.698 0.598 -7.400 5.517 -1.998 -1.853 H6N2 A38 36 A38 H2 H2 H 0 1 N N N 0.641 1.521 -3.061 5.312 0.244 2.925 H2 A38 37 # 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 A38 O3P P SING N N 1 A38 O3P H3P SING N N 2 A38 P O1P DOUB N N 3 A38 P O2P SING N N 4 A38 P "O5'" SING N N 5 A38 O2P H2P SING N N 6 A38 "O5'" "C5'" SING N N 7 A38 "C5'" "C4'" SING N N 8 A38 "C5'" "H5'1" SING N N 9 A38 "C5'" "H5'2" SING N N 10 A38 "C4'" "O4'" SING N N 11 A38 "C4'" "C3'" SING N N 12 A38 "C4'" "H4'" SING N N 13 A38 "O4'" "C1'" SING N N 14 A38 "C3'" "O3'" SING N N 15 A38 "C3'" "C2'" SING N N 16 A38 "C3'" "H3'" SING N N 17 A38 "O3'" HA SING N N 18 A38 "C2'" "C1'" SING N N 19 A38 "C2'" "H2'1" SING N N 20 A38 "C2'" "H2'2" SING N N 21 A38 "C1'" N9 SING N N 22 A38 "C1'" "H1'" SING N N 23 A38 N9 C8 SING N N 24 A38 N9 C4 SING N N 25 A38 C8 N7 SING N N 26 A38 C8 O DOUB N N 27 A38 N7 C5 SING N N 28 A38 N7 H7 SING N N 29 A38 C5 C6 DOUB Y N 30 A38 C5 C4 SING Y N 31 A38 C6 N6 SING N N 32 A38 C6 N1 SING Y N 33 A38 N6 H6N1 SING N N 34 A38 N6 H6N2 SING N N 35 A38 N1 C2 DOUB Y N 36 A38 C2 N3 SING Y N 37 A38 C2 H2 SING N N 38 A38 N3 C4 DOUB Y N 39 # 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 A38 SMILES ACDLabs 10.04 "O=C2Nc1c(ncnc1N2C3OC(C(O)C3)COP(=O)(O)O)N" A38 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2N([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)C(=O)Nc12" A38 SMILES CACTVS 3.341 "Nc1ncnc2N([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)C(=O)Nc12" A38 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N" A38 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)N(C(=O)N2)C3CC(C(O3)COP(=O)(O)O)O)N" A38 InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-8-7-9(13-3-12-8)15(10(17)14-7)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H,14,17)(H2,11,12,13)(H2,18,19,20)/t4-,5+,6+/m0/s1" A38 InChIKey InChI 1.03 QFGWDFAYOAGQDH-KVQBGUIXSA-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 A38 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-8-oxoadenosine 5'-(dihydrogen phosphate) ; A38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-amino-8-oxo-7H-purin-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 A38 "Create component" 1996-06-10 RCSB A38 "Modify descriptor" 2011-06-04 RCSB #