data_3DG # _chem_comp.id 3DG _chem_comp.name "9-(3-DEOXY-BETA-D-RIBOFURANOSYL)GUANINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 3-DEOXYGUANOSINE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-11-10 _chem_comp.pdbx_modified_date 2020-06-17 _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 267.241 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3DG _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 1V45 _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 3DG N9 N9 N 0 1 Y N N 53.233 129.076 55.619 0.071 -0.460 -0.007 N9 3DG 1 3DG "C1'" "C1'" C 0 1 N N R 52.802 128.394 56.889 1.258 0.359 -0.263 "C1'" 3DG 2 3DG "C2'" "C2'" C 0 1 N N R 53.813 127.833 57.974 1.638 1.164 0.999 "C2'" 3DG 3 3DG "C3'" "C3'" C 0 1 N N N 53.437 128.553 59.373 3.185 1.157 0.995 "C3'" 3DG 4 3DG "C4'" "C4'" C 0 1 N N S 52.490 129.694 58.890 3.553 0.353 -0.271 "C4'" 3DG 5 3DG "O4'" "O4'" O 0 1 N N N 51.923 129.314 57.602 2.402 -0.481 -0.527 "O4'" 3DG 6 3DG "C5'" "C5'" C 0 1 N N N 53.147 131.050 58.636 4.790 -0.511 -0.015 "C5'" 3DG 7 3DG "O5'" "O5'" O 0 1 N N N 52.082 131.925 58.150 5.138 -1.212 -1.211 "O5'" 3DG 8 3DG "O2'" "O2'" O 0 1 N N N 53.584 126.393 58.115 1.143 2.502 0.916 "O2'" 3DG 9 3DG C8 C8 C 0 1 Y N N 52.268 129.617 54.781 0.062 -1.762 0.405 C8 3DG 10 3DG N7 N7 N 0 1 Y N N 52.924 130.175 53.725 -1.165 -2.176 0.532 N7 3DG 11 3DG C5 C5 C 0 1 Y N N 54.258 129.966 53.966 -2.013 -1.169 0.211 C5 3DG 12 3DG C6 C6 C 0 1 N N N 55.315 130.367 53.174 -3.422 -1.045 0.167 C6 3DG 13 3DG O6 O6 O 0 1 N N N 55.226 131.026 52.099 -4.142 -1.983 0.462 O6 3DG 14 3DG N1 N1 N 0 1 N N N 56.556 129.969 53.717 -3.950 0.143 -0.205 N1 3DG 15 3DG C2 C2 C 0 1 N N N 56.700 129.258 54.895 -3.136 1.184 -0.538 C2 3DG 16 3DG N2 N2 N 0 1 N N N 57.946 128.970 55.308 -3.700 2.376 -0.917 N2 3DG 17 3DG N3 N3 N 0 1 N N N 55.681 128.872 55.656 -1.826 1.081 -0.501 N3 3DG 18 3DG C4 C4 C 0 1 Y N N 54.499 129.257 55.132 -1.232 -0.062 -0.137 C4 3DG 19 3DG "H1'" "H1'" H 0 1 N N N 52.387 127.451 56.464 1.079 1.032 -1.103 "H1'" 3DG 20 3DG "H2'" "H2'" H 0 1 N N N 54.874 128.023 57.688 1.256 0.672 1.894 "H2'" 3DG 21 3DG "H3'1" "1H3'" H 0 0 N N N 54.307 128.884 59.987 3.568 0.663 1.887 "H3'1" 3DG 22 3DG "H3'2" "2H3'" H 0 0 N N N 53.012 127.881 60.155 3.570 2.175 0.926 "H3'2" 3DG 23 3DG "H4'" "H4'" H 0 1 N N N 51.760 129.812 59.724 3.729 1.025 -1.111 "H4'" 3DG 24 3DG "H5'1" "1H5'" H 0 0 N N N 54.027 130.998 57.954 5.621 0.126 0.288 "H5'1" 3DG 25 3DG "H5'2" "2H5'" H 0 0 N N N 53.688 131.456 59.522 4.575 -1.228 0.777 "H5'2" 3DG 26 3DG "H5'" "H5'" H 0 1 N N N 52.491 132.768 57.992 5.920 -1.743 -1.006 "H5'" 3DG 27 3DG H1 H1 H 0 1 N N N 54.190 126.057 58.765 1.464 2.968 1.700 H1 3DG 28 3DG H8 H8 H 0 1 N N N 51.175 129.606 54.928 0.942 -2.358 0.596 H8 3DG 29 3DG HN1 HN1 H 0 1 N N N 57.413 130.214 53.221 -4.913 0.252 -0.242 HN1 3DG 30 3DG HN21 1HN2 H 0 0 N N N 58.486 129.833 55.370 -3.133 3.127 -1.153 HN21 3DG 31 3DG HN22 2HN2 H 0 0 N N N 58.052 128.446 56.177 -4.665 2.466 -0.953 HN22 3DG 32 # # 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 3DG N9 "C1'" SING N N 1 3DG N9 C8 SING Y N 2 3DG N9 C4 SING Y N 3 3DG "C1'" "C2'" SING N N 4 3DG "C1'" "O4'" SING N N 5 3DG "C1'" "H1'" SING N N 6 3DG "C2'" "C3'" SING N N 7 3DG "C2'" "O2'" SING N N 8 3DG "C2'" "H2'" SING N N 9 3DG "C3'" "C4'" SING N N 10 3DG "C3'" "H3'1" SING N N 11 3DG "C3'" "H3'2" SING N N 12 3DG "C4'" "O4'" SING N N 13 3DG "C4'" "C5'" SING N N 14 3DG "C4'" "H4'" SING N N 15 3DG "C5'" "O5'" SING N N 16 3DG "C5'" "H5'1" SING N N 17 3DG "C5'" "H5'2" SING N N 18 3DG "O5'" "H5'" SING N N 19 3DG "O2'" H1 SING N N 20 3DG C8 N7 DOUB Y N 21 3DG C8 H8 SING N N 22 3DG N7 C5 SING Y N 23 3DG C5 C6 SING N N 24 3DG C5 C4 DOUB Y N 25 3DG C6 O6 DOUB N N 26 3DG C6 N1 SING N N 27 3DG N1 C2 SING N N 28 3DG N1 HN1 SING N N 29 3DG C2 N2 SING N N 30 3DG C2 N3 DOUB N N 31 3DG N2 HN21 SING N N 32 3DG N2 HN22 SING N N 33 3DG N3 C4 SING N N 34 # # 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 3DG SMILES ACDLabs 10.04 "O=C1c2ncn(c2N=C(N)N1)C3OC(CC3O)CO" 3DG SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)C[C@H]3O" 3DG SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)C[CH]3O" 3DG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H](C[C@H](O3)CO)O)N=C(NC2=O)N" 3DG SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(CC(O3)CO)O)N=C(NC2=O)N" 3DG InChI InChI 1.03 "InChI=1S/C10H13N5O4/c11-10-13-7-6(8(18)14-10)12-3-15(7)9-5(17)1-4(2-16)19-9/h3-5,9,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5+,9+/m0/s1" 3DG InChIKey InChI 1.03 OROIAVZITJBGSM-OBXARNEKSA-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 3DG "SYSTEMATIC NAME" ACDLabs 10.04 "3'-deoxyguanosine" 3DG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-amino-9-[(2R,3R,5S)-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-purin-6-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3DG "Create component" 2003-11-10 RCSB 3DG "Modify descriptor" 2011-06-04 RCSB 3DG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3DG _pdbx_chem_comp_synonyms.name 3-DEOXYGUANOSINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##