data_SDG # _chem_comp.id SDG _chem_comp.name "2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purine-6-selenol" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O6 P Se" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-12-07 _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 410.182 _chem_comp.one_letter_code G _chem_comp.three_letter_code SDG _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 2R7Y _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 SDG O3P O3P O 0 1 N Y N 23.074 2.635 20.883 -6.127 2.011 -1.726 O3P SDG 1 SDG C2 C2 C 0 1 Y N N 15.062 5.438 25.453 3.815 -1.911 -0.947 C2 SDG 2 SDG P P P 0 1 N N N 23.193 3.977 20.005 -5.870 1.235 -0.339 P SDG 3 SDG O1P O1P O 0 1 N N N 23.295 3.515 18.588 -5.622 2.219 0.738 O1P SDG 4 SDG O2P O2P O 0 1 N N N 24.251 4.877 20.582 -7.165 0.351 0.029 O2P SDG 5 SDG "O5'" "O5'" O 0 1 N N N 21.775 4.650 20.215 -4.589 0.272 -0.492 "O5'" SDG 6 SDG N9 N9 N 0 1 Y N N 18.368 5.603 24.116 0.642 -0.412 0.022 N9 SDG 7 SDG C4 C4 C 0 1 Y N N 17.229 5.454 24.896 1.931 -0.778 -0.275 C4 SDG 8 SDG N3 N3 N 0 1 Y N N 15.950 5.518 24.458 2.504 -1.865 -0.775 N3 SDG 9 SDG N2 N2 N 0 1 N N N 13.743 5.483 25.182 4.381 -3.060 -1.477 N2 SDG 10 SDG N1 N1 N 0 1 Y N N 15.391 5.313 26.787 4.606 -0.892 -0.633 N1 SDG 11 SDG C6 C6 C 0 1 Y N N 16.689 5.247 27.279 4.115 0.227 -0.130 C6 SDG 12 SDG SE SE SE 0 0 N N N 17.002 5.151 29.060 5.299 1.720 0.326 SE SDG 13 SDG C5 C5 C 0 1 Y N N 17.686 5.303 26.194 2.737 0.324 0.070 C5 SDG 14 SDG N7 N7 N 0 1 Y N N 19.076 5.262 26.227 1.909 1.286 0.550 N7 SDG 15 SDG C8 C8 C 0 1 Y N N 19.439 5.419 24.972 0.682 0.856 0.522 C8 SDG 16 SDG "C2'" "C2'" C 0 1 N N N 18.783 7.460 22.601 -0.770 -2.158 1.053 "C2'" SDG 17 SDG "C5'" "C5'" C 0 1 N N N 21.596 5.807 21.021 -4.041 -0.474 0.596 "C5'" SDG 18 SDG "C4'" "C4'" C 0 1 N N R 20.118 6.077 21.150 -2.836 -1.280 0.108 "C4'" SDG 19 SDG "O4'" "O4'" O 0 1 N N N 19.548 5.301 22.243 -1.736 -0.399 -0.205 "O4'" SDG 20 SDG "C1'" "C1'" C 0 1 N N R 18.392 5.992 22.697 -0.557 -1.232 -0.165 "C1'" SDG 21 SDG "C3'" "C3'" C 0 1 N N S 19.730 7.534 21.405 -2.304 -2.190 1.237 "C3'" SDG 22 SDG "O3'" "O3'" O 0 1 N N N 19.054 8.037 20.248 -2.799 -3.522 1.082 "O3'" SDG 23 SDG HO3P HO3P H 0 0 N N N 23.051 1.880 20.307 -6.885 2.611 -1.706 HO3P SDG 24 SDG HO2P HO2P H 0 0 N N N 24.903 5.067 19.917 -7.387 -0.316 -0.635 HO2P SDG 25 SDG HN2 HN2 H 0 1 N N N 13.226 5.494 26.038 5.340 -3.109 -1.613 HN2 SDG 26 SDG HN2A HN2A H 0 0 N N N 13.538 6.310 24.659 3.818 -3.814 -1.712 HN2A SDG 27 SDG H8 H8 H 0 1 N N N 20.468 5.406 24.644 -0.179 1.420 0.848 H8 SDG 28 SDG "H2'" "H2'" H 0 1 N N N 19.282 7.797 23.522 -0.390 -3.158 0.844 "H2'" SDG 29 SDG "H2'A" "H2'A" H 0 0 N N N 17.907 8.114 22.476 -0.286 -1.744 1.937 "H2'A" SDG 30 SDG "H5'" "H5'" H 0 1 N N N 22.032 5.638 22.017 -3.726 0.211 1.384 "H5'" SDG 31 SDG "H5'A" "H5'A" H 0 0 N N N 22.097 6.670 20.557 -4.798 -1.154 0.988 "H5'A" SDG 32 SDG "H4'" "H4'" H 0 1 N N N 19.721 5.791 20.165 -3.107 -1.875 -0.764 "H4'" SDG 33 SDG "H1'" "H1'" H 0 1 N N N 17.444 5.800 22.174 -0.477 -1.821 -1.079 "H1'" SDG 34 SDG "H3'" "H3'" H 0 1 N N N 20.586 8.197 21.601 -2.581 -1.790 2.212 "H3'" SDG 35 SDG "HO3'" "HO3'" H 0 0 N Y N 18.131 8.148 20.443 -2.496 -4.136 1.764 "HO3'" SDG 36 SDG HSE HSE H 0 1 N N N 18.481 5.124 29.308 5.313 2.511 -1.019 HSE SDG 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 SDG P O3P SING N N 1 SDG O3P HO3P SING N N 2 SDG N3 C2 DOUB Y N 3 SDG N2 C2 SING N N 4 SDG C2 N1 SING Y N 5 SDG O1P P DOUB N N 6 SDG P "O5'" SING N N 7 SDG P O2P SING N N 8 SDG O2P HO2P SING N N 9 SDG "O5'" "C5'" SING N N 10 SDG "C1'" N9 SING N N 11 SDG N9 C4 SING Y N 12 SDG N9 C8 SING Y N 13 SDG N3 C4 SING Y N 14 SDG C4 C5 DOUB Y N 15 SDG N2 HN2 SING N N 16 SDG N2 HN2A SING N N 17 SDG N1 C6 DOUB Y N 18 SDG C5 C6 SING Y N 19 SDG C6 SE SING N N 20 SDG C5 N7 SING Y N 21 SDG C8 N7 DOUB Y N 22 SDG C8 H8 SING N N 23 SDG "C3'" "C2'" SING N N 24 SDG "C2'" "C1'" SING N N 25 SDG "C2'" "H2'" SING N N 26 SDG "C2'" "H2'A" SING N N 27 SDG "C5'" "C4'" SING N N 28 SDG "C5'" "H5'" SING N N 29 SDG "C5'" "H5'A" SING N N 30 SDG "C4'" "C3'" SING N N 31 SDG "C4'" "O4'" SING N N 32 SDG "C4'" "H4'" SING N N 33 SDG "O4'" "C1'" SING N N 34 SDG "C1'" "H1'" SING N N 35 SDG "O3'" "C3'" SING N N 36 SDG "C3'" "H3'" SING N N 37 SDG "O3'" "HO3'" SING N N 38 SDG SE HSE SING N 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 SDG SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c([SeH])nc(nc12)N)CC3O" SDG SMILES_CANONICAL CACTVS 3.341 "Nc1nc([SeH])c2ncn([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)c2n1" SDG SMILES CACTVS 3.341 "Nc1nc([SeH])c2ncn([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)c2n1" SDG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)nc(nc2[SeH])N" SDG SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)nc(nc2[SeH])N" SDG InChI InChI 1.03 "InChI=1S/C10H14N5O6PSe/c11-10-13-8-7(9(23)14-10)12-3-15(8)6-1-4(16)5(21-6)2-20-22(17,18)19/h3-6,16H,1-2H2,(H2,17,18,19)(H3,11,13,14,23)/t4-,5+,6+/m0/s1" SDG InChIKey InChI 1.03 RNSTWFSCXYEWJZ-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 SDG "SYSTEMATIC NAME" ACDLabs 10.04 "2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purine-6-selenol" SDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2-amino-6-selanyl-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 SDG "Create component" 2007-12-07 RCSB SDG "Modify aromatic_flag" 2011-06-04 RCSB SDG "Modify descriptor" 2011-06-04 RCSB #