data_3D1 # _chem_comp.id 3D1 _chem_comp.name "(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 N5 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-DEOXYADENOSINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-02-16 _chem_comp.pdbx_modified_date 2021-03-01 _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 251.242 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3D1 _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 1S2G _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 3D1 "O5'" "O5'" O 0 1 N N N -1.376 -10.273 -22.038 4.569 1.772 1.047 "O5'" 3D1 1 3D1 "C5'" "C5'" C 0 1 N N N -2.028 -9.017 -22.262 4.217 0.988 -0.094 "C5'" 3D1 2 3D1 "C4'" "C4'" C 0 1 N N R -2.338 -8.253 -20.946 3.184 -0.067 0.310 "C4'" 3D1 3 3D1 "O4'" "O4'" O 0 1 N N N -1.147 -7.957 -20.184 1.940 0.560 0.689 "O4'" 3D1 4 3D1 "C1'" "C1'" C 0 1 N N R -0.721 -6.618 -20.530 0.912 -0.437 0.559 "C1'" 3D1 5 3D1 N9 N9 N 0 1 Y N N 0.371 -6.662 -21.829 -0.339 0.191 0.126 N9 3D1 6 3D1 C4 C4 C 0 1 Y N N 0.788 -5.643 -22.680 -1.604 -0.302 0.319 C4 3D1 7 3D1 N3 N3 N 0 1 Y N N 0.397 -4.324 -22.647 -2.110 -1.388 0.893 N3 3D1 8 3D1 C2 C2 C 0 1 Y N N 0.994 -3.586 -23.634 -3.411 -1.589 0.920 C2 3D1 9 3D1 N1 N1 N 0 1 Y N N 1.887 -4.047 -24.579 -4.271 -0.738 0.389 N1 3D1 10 3D1 C6 C6 C 0 1 Y N N 2.255 -5.410 -24.567 -3.858 0.376 -0.206 C6 3D1 11 3D1 N6 N6 N 0 1 N N N 3.102 -5.949 -25.431 -4.766 1.261 -0.761 N6 3D1 12 3D1 C5 C5 C 0 1 Y N N 1.698 -6.248 -23.590 -2.477 0.634 -0.261 C5 3D1 13 3D1 N7 N7 N 0 1 Y N N 1.898 -7.611 -23.368 -1.714 1.631 -0.768 N7 3D1 14 3D1 C8 C8 C 0 1 Y N N 1.121 -7.799 -22.352 -0.459 1.377 -0.537 C8 3D1 15 3D1 "C2'" "C2'" C 0 1 N N N -1.945 -5.876 -21.032 1.386 -1.447 -0.503 "C2'" 3D1 16 3D1 "C3'" "C3'" C 0 1 N N S -3.006 -6.915 -21.302 2.793 -0.943 -0.907 "C3'" 3D1 17 3D1 "O3'" "O3'" O 0 1 N N N -4.146 -6.607 -20.480 3.701 -2.035 -1.062 "O3'" 3D1 18 3D1 "H5'" "H5'" H 0 1 N N N -1.232 -10.708 -22.870 5.221 2.462 0.863 "H5'" 3D1 19 3D1 "H5'1" "H5'1" H 0 0 N N N -1.368 -8.390 -22.879 3.793 1.634 -0.863 "H5'1" 3D1 20 3D1 "H5'2" "H5'2" H 0 0 N N N -2.987 -9.225 -22.759 5.107 0.494 -0.485 "H5'2" 3D1 21 3D1 "H4'" "H4'" H 0 1 N N N -2.989 -8.897 -20.337 3.567 -0.684 1.123 "H4'" 3D1 22 3D1 "H1'" "H1'" H 0 1 N N N -0.253 -6.146 -19.654 0.762 -0.942 1.513 "H1'" 3D1 23 3D1 H2 H2 H 0 1 N N N 0.740 -2.537 -23.677 -3.790 -2.482 1.395 H2 3D1 24 3D1 HN61 HN61 H 0 0 N N N 2.642 -6.085 -26.309 -5.716 1.071 -0.717 HN61 3D1 25 3D1 HN62 HN62 H 0 0 N N N 3.884 -5.339 -25.556 -4.452 2.070 -1.193 HN62 3D1 26 3D1 H8 H8 H 0 1 N N N 1.029 -8.776 -21.900 0.366 2.009 -0.829 H8 3D1 27 3D1 "H2'1" "H2'1" H 0 0 N N N -2.295 -5.159 -20.275 1.447 -2.449 -0.077 "H2'1" 3D1 28 3D1 "H2'2" "H2'2" H 0 0 N N N -1.712 -5.306 -21.943 0.716 -1.439 -1.364 "H2'2" 3D1 29 3D1 "H3'" "H3'" H 0 1 N N N -3.371 -6.949 -22.339 2.745 -0.345 -1.817 "H3'" 3D1 30 3D1 H1 H1 H 0 1 N N N -3.874 -6.539 -19.572 3.497 -2.612 -1.811 H1 3D1 31 # # 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 3D1 "O5'" "C5'" SING N N 1 3D1 "O5'" "H5'" SING N N 2 3D1 "C5'" "C4'" SING N N 3 3D1 "C5'" "H5'1" SING N N 4 3D1 "C5'" "H5'2" SING N N 5 3D1 "C4'" "O4'" SING N N 6 3D1 "C4'" "C3'" SING N N 7 3D1 "C4'" "H4'" SING N N 8 3D1 "O4'" "C1'" SING N N 9 3D1 "C1'" N9 SING N N 10 3D1 "C1'" "C2'" SING N N 11 3D1 "C1'" "H1'" SING N N 12 3D1 N9 C4 SING Y N 13 3D1 N9 C8 SING Y N 14 3D1 C4 N3 DOUB Y N 15 3D1 C4 C5 SING Y N 16 3D1 N3 C2 SING Y N 17 3D1 C2 N1 DOUB Y N 18 3D1 C2 H2 SING N N 19 3D1 N1 C6 SING Y N 20 3D1 C6 N6 SING N N 21 3D1 C6 C5 DOUB Y N 22 3D1 N6 HN61 SING N N 23 3D1 N6 HN62 SING N N 24 3D1 C5 N7 SING Y N 25 3D1 N7 C8 DOUB Y N 26 3D1 C8 H8 SING N N 27 3D1 "C2'" "C3'" SING N N 28 3D1 "C2'" "H2'1" SING N N 29 3D1 "C2'" "H2'2" SING N N 30 3D1 "C3'" "O3'" SING N N 31 3D1 "C3'" "H3'" SING N N 32 3D1 "O3'" H1 SING N N 33 # # 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 3D1 SMILES ACDLabs 10.04 "n2c1c(ncnc1n(c2)C3OC(C(O)C3)CO)N" 3D1 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3" 3D1 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO)O3" 3D1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O)N" 3D1 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)CO)O)N" 3D1 InChI InChI 1.03 "InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1" 3D1 InChIKey InChI 1.03 OLXZPDWKRNYJJZ-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 3D1 "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxyadenosine" 3D1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3D1 "Create component" 2004-02-16 RCSB 3D1 "Modify descriptor" 2011-06-04 RCSB 3D1 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3D1 _pdbx_chem_comp_synonyms.name "2'-DEOXYADENOSINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##