data_OGX # _chem_comp.id OGX _chem_comp.name "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H19 N6 O7 P S" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-09-10 _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 422.354 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OGX _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 3JR5 _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 OGX OP2 OP2 O 0 1 N Y N N N N -16.137 53.340 29.650 3.354 -3.085 0.212 OP2 OGX 1 OGX P P P 0 1 N N N N N N -15.057 52.189 29.496 3.711 -1.884 -0.576 P OGX 2 OGX S S S 0 1 N N N N N N -11.150 51.253 29.128 6.448 2.540 -0.720 S OGX 3 OGX N1 N1 N 0 1 N N N N N N -21.635 53.602 25.620 -6.333 0.229 -1.192 N1 OGX 4 OGX C2 C2 C 0 1 N N N N N N -20.355 54.089 25.805 -5.427 1.145 -1.631 C2 OGX 5 OGX N2 N2 N 0 1 N N N N N N -20.219 55.223 26.518 -5.803 2.049 -2.592 N2 OGX 6 OGX N3 N3 N 0 1 N N N N N N -19.273 53.490 25.318 -4.201 1.187 -1.157 N3 OGX 7 OGX C4 C4 C 0 1 N N N N N N -19.548 52.361 24.620 -3.793 0.324 -0.219 C4 OGX 8 OGX N4 N4 N 0 1 N N N N N N -13.507 52.577 29.724 5.148 -1.235 0.010 N4 OGX 9 OGX C5 C5 C 0 1 N N N N N N -20.790 51.824 24.377 -4.678 -0.632 0.264 C5 OGX 10 OGX C6 C6 C 0 1 N N N N N N -21.946 52.442 24.911 -5.985 -0.667 -0.242 C6 OGX 11 OGX O6 O6 O 0 1 N N N N N N -23.124 52.085 24.815 -6.788 -1.494 0.160 O6 OGX 12 OGX N7 N7 N 0 1 N N N N N N -20.611 50.676 23.612 -3.987 -1.381 1.220 N7 OGX 13 OGX C8 C8 C 0 1 N N N N N N -19.336 50.513 23.379 -2.735 -0.889 1.304 C8 OGX 14 OGX O8 O8 O 0 1 N N N N N N -18.793 49.620 22.729 -1.863 -1.309 2.041 O8 OGX 15 OGX N9 N9 N 0 1 N N N N N N -18.639 51.539 23.983 -2.598 0.139 0.445 N9 OGX 16 OGX "C1'" "C1'" C 0 1 N N R N N N -17.185 51.619 23.987 -1.381 0.930 0.248 "C1'" OGX 17 OGX "C2'" "C2'" C 0 1 N N N N N N -16.379 52.796 24.525 -1.048 1.709 1.535 "C2'" OGX 18 OGX "C3'" "C3'" C 0 1 N N S N N N -15.151 52.059 25.054 0.371 1.223 1.916 "C3'" OGX 19 OGX "O3'" "O3'" O 0 1 N N N N N N -14.360 51.520 23.967 1.179 2.312 2.369 "O3'" OGX 20 OGX "C4'" "C4'" C 0 1 N N R N N N -15.848 50.962 25.848 0.897 0.667 0.569 "C4'" OGX 21 OGX "O4'" "O4'" O 0 1 N N N N N N -17.023 50.650 25.049 -0.270 0.058 -0.023 "O4'" OGX 22 OGX "C5'" "C5'" C 0 1 N N N N N N -16.224 51.396 27.268 1.988 -0.379 0.807 "C5'" OGX 23 OGX "O5'" "O5'" O 0 1 N N N N N N -15.049 51.748 27.945 2.536 -0.790 -0.448 "O5'" OGX 24 OGX "C7'" "C7'" C 0 1 N N N N N N -12.871 52.378 31.024 5.534 -0.038 -0.750 "C7'" OGX 25 OGX "C8'" "C8'" C 0 1 N N N N N N -11.779 51.330 30.847 5.971 1.063 0.219 "C8'" OGX 26 OGX OP1 OP1 O 0 1 N N N N N N -15.545 51.064 30.330 3.897 -2.292 -2.122 OP1 OGX 27 OGX HS HS H 0 1 N N N N N N -10.252 50.317 29.211 6.802 3.409 0.243 HS OGX 28 OGX HN1 HN1 H 0 1 N N N N N N -22.391 54.118 26.023 -7.231 0.221 -1.559 HN1 OGX 29 OGX HN2 HN2 H 0 1 N N N N N N -19.310 55.608 26.677 -6.704 2.030 -2.951 HN2 OGX 30 OGX HN2A HN2A H 0 0 N N N N N N -21.027 55.681 26.888 -5.167 2.708 -2.914 HN2A OGX 31 OGX HN4 HN4 H 0 1 N N N N N N -12.987 52.019 29.077 5.077 -1.030 0.996 HN4 OGX 32 OGX HN7 HN7 H 0 1 N N N N N N -21.341 50.072 23.292 -4.344 -2.123 1.732 HN7 OGX 33 OGX "H1'" "H1'" H 0 1 N N N N N N -16.841 51.573 22.943 -1.520 1.624 -0.581 "H1'" OGX 34 OGX "H2'" "H2'" H 0 1 N N N N N N -16.130 53.532 23.746 -1.045 2.782 1.341 "H2'" OGX 35 OGX "H2'A" "H2'A" H 0 0 N N N N N N -16.912 53.353 25.310 -1.760 1.465 2.323 "H2'A" OGX 36 OGX "H3'" "H3'" H 0 1 N N N N N N -14.437 52.667 25.628 0.324 0.436 2.670 "H3'" OGX 37 OGX "HO3'" "HO3'" H 0 0 N Y N N N N -13.603 51.067 24.320 0.839 2.750 3.161 "HO3'" OGX 38 OGX "H4'" "H4'" H 0 1 N N N N N N -15.192 50.093 26.006 1.273 1.475 -0.060 "H4'" OGX 39 OGX "H5'" "H5'" H 0 1 N N N N N N -16.905 52.259 27.227 2.777 0.052 1.424 "H5'" OGX 40 OGX "H5'A" "H5'A" H 0 0 N N N N N N -16.724 50.568 27.792 1.559 -1.242 1.315 "H5'A" OGX 41 OGX "H7'" "H7'" H 0 1 N N N N N N -12.434 53.323 31.380 6.360 -0.283 -1.418 "H7'" OGX 42 OGX "H7'A" "H7'A" H 0 0 N N N N N N -13.613 52.031 31.759 4.684 0.310 -1.336 "H7'A" OGX 43 OGX "H8'" "H8'" H 0 1 N N N N N N -12.195 50.346 31.110 6.821 0.715 0.805 "H8'" OGX 44 OGX "H8'A" "H8'A" H 0 0 N N N N N N -10.941 51.584 31.513 5.145 1.307 0.887 "H8'A" OGX 45 OGX HOP1 HOP1 H 0 0 N N N N N N -16.366 51.307 30.741 4.132 -1.553 -2.699 HOP1 OGX 46 # 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 OGX P OP2 DOUB N N 1 OGX "O5'" P SING N N 2 OGX P N4 SING N N 3 OGX P OP1 SING N N 4 OGX S "C8'" SING N N 5 OGX S HS SING N N 6 OGX C6 N1 SING N N 7 OGX N1 C2 SING N N 8 OGX N1 HN1 SING N N 9 OGX N3 C2 DOUB N N 10 OGX C2 N2 SING N N 11 OGX N2 HN2 SING N N 12 OGX N2 HN2A SING N N 13 OGX C4 N3 SING N N 14 OGX N9 C4 SING N N 15 OGX C5 C4 DOUB N N 16 OGX N4 "C7'" SING N N 17 OGX N4 HN4 SING N N 18 OGX N7 C5 SING N N 19 OGX C5 C6 SING N N 20 OGX O6 C6 DOUB N N 21 OGX C8 N7 SING N N 22 OGX N7 HN7 SING N N 23 OGX O8 C8 DOUB N N 24 OGX C8 N9 SING N N 25 OGX N9 "C1'" SING N N 26 OGX "C1'" "C2'" SING N N 27 OGX "C1'" "O4'" SING N N 28 OGX "C1'" "H1'" SING N N 29 OGX "C2'" "C3'" SING N N 30 OGX "C2'" "H2'" SING N N 31 OGX "C2'" "H2'A" SING N N 32 OGX "O3'" "C3'" SING N N 33 OGX "C3'" "C4'" SING N N 34 OGX "C3'" "H3'" SING N N 35 OGX "O3'" "HO3'" SING N N 36 OGX "O4'" "C4'" SING N N 37 OGX "C4'" "C5'" SING N N 38 OGX "C4'" "H4'" SING N N 39 OGX "C5'" "O5'" SING N N 40 OGX "C5'" "H5'" SING N N 41 OGX "C5'" "H5'A" SING N N 42 OGX "C8'" "C7'" SING N N 43 OGX "C7'" "H7'" SING N N 44 OGX "C7'" "H7'A" SING N N 45 OGX "C8'" "H8'" SING N N 46 OGX "C8'" "H8'A" SING N N 47 OGX OP1 HOP1 SING N N 48 # 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 OGX SMILES ACDLabs 11.02 "O=P(O)(OCC3OC(N2C(=O)NC1=C2N=C(N)NC1=O)CC3O)NCCS" OGX SMILES_CANONICAL CACTVS 3.352 "NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O3)C(=O)N1" OGX SMILES CACTVS 3.352 "NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)NCCS)O3)C(=O)N1" OGX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(NCCS)O)O" OGX SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(NCCS)O)O" OGX InChI InChI 1.03 "InChI=1S/C12H19N6O7PS/c13-11-16-9-8(10(20)17-11)15-12(21)18(9)7-3-5(19)6(25-7)4-24-26(22,23)14-1-2-27/h5-7,19,27H,1-4H2,(H,15,21)(H2,14,22,23)(H3,13,16,17,20)/t5-,6+,7+/m0/s1" OGX InChIKey InChI 1.03 QTNBODRGZGXUEH-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 OGX "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine" OGX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site OGX "Create component" 2009-09-10 RCSB OGX "Modify descriptor" 2011-06-04 RCSB OGX "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id OGX _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom S _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? _pdbx_chem_comp_pcm.first_instance_model_db_code 3JR5 #