data_GX1 # _chem_comp.id GX1 _chem_comp.name "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}guanosine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H19 N6 O6 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 2009-09-09 _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 406.355 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GX1 _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 3JR4 _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 GX1 OP2 OP2 O 0 1 N Y N -15.996 53.680 30.170 3.624 -2.965 0.790 OP2 GX1 1 GX1 P P P 0 1 N N N -14.760 52.668 30.232 3.871 -1.876 -0.182 P GX1 2 GX1 S S S 0 1 N N N -11.424 51.380 29.704 6.178 2.707 -1.049 S GX1 3 GX1 N1 N1 N 0 1 N N N -20.282 55.756 27.742 -6.574 0.348 -0.709 N1 GX1 4 GX1 C2 C2 C 0 1 N N N -19.592 55.705 26.524 -5.723 1.406 -0.826 C2 GX1 5 GX1 N2 N2 N 0 1 N N N -19.646 56.746 25.703 -6.221 2.618 -1.235 N2 GX1 6 GX1 N3 N3 N 0 1 N N N -18.878 54.619 26.181 -4.441 1.300 -0.559 N3 GX1 7 GX1 C4 C4 C 0 1 Y N N -18.806 53.551 26.993 -3.912 0.138 -0.158 C4 GX1 8 GX1 N4 N4 N 0 1 N N N -13.372 53.147 30.932 5.236 -1.009 0.282 N4 GX1 9 GX1 C5 C5 C 0 1 Y N N -19.474 53.551 28.215 -4.734 -0.986 -0.018 C5 GX1 10 GX1 C6 C6 C 0 1 N N N -20.221 54.660 28.602 -6.112 -0.858 -0.309 C6 GX1 11 GX1 O6 O6 O 0 1 N N N -20.818 54.680 29.677 -6.866 -1.809 -0.196 O6 GX1 12 GX1 N7 N7 N 0 1 Y N N -19.229 52.382 28.799 -3.948 -2.010 0.395 N7 GX1 13 GX1 C8 C8 C 0 1 Y N N -18.447 51.672 27.986 -2.722 -1.591 0.514 C8 GX1 14 GX1 N9 N9 N 0 1 Y N N -18.183 52.378 26.883 -2.651 -0.269 0.183 N9 GX1 15 GX1 "C1'" "C1'" C 0 1 N N R -17.337 51.939 25.733 -1.445 0.563 0.191 "C1'" GX1 16 GX1 "C2'" "C2'" C 0 1 N N N -16.412 53.109 25.347 -1.284 1.263 1.559 "C2'" GX1 17 GX1 "C3'" "C3'" C 0 1 N N S -15.005 52.569 25.574 0.241 1.252 1.810 "C3'" GX1 18 GX1 "O3'" "O3'" O 0 1 N N N -14.520 52.055 24.333 0.742 2.586 1.908 "O3'" GX1 19 GX1 "C4'" "C4'" C 0 1 N N R -15.241 51.414 26.551 0.821 0.546 0.564 "C4'" GX1 20 GX1 "O4'" "O4'" O 0 1 N N N -16.453 50.822 26.059 -0.266 -0.260 0.057 "O4'" GX1 21 GX1 "C5'" "C5'" C 0 1 N N N -15.588 51.864 27.965 2.004 -0.341 0.957 "C5'" GX1 22 GX1 "O5'" "O5'" O 0 1 N N N -14.494 52.370 28.689 2.598 -0.892 -0.220 "O5'" GX1 23 GX1 "C7'" "C7'" C 0 1 N N N -12.729 52.357 31.998 5.513 0.082 -0.661 "C7'" GX1 24 GX1 "C8'" "C8'" C 0 1 N N N -12.055 51.120 31.403 5.836 1.360 0.116 "C8'" GX1 25 GX1 OP1 OP1 O 0 1 N N N -15.246 51.413 30.852 4.107 -2.506 -1.645 OP1 GX1 26 GX1 HS HS H 0 1 N N N -10.910 50.219 29.426 6.441 3.748 -0.239 HS GX1 27 GX1 HN1 HN1 H 0 1 N N N -20.811 56.567 27.991 -7.516 0.461 -0.910 HN1 GX1 28 GX1 HN2 HN2 H 0 1 N N N -19.156 56.721 24.831 -7.165 2.713 -1.436 HN2 GX1 29 GX1 HN2A HN2A H 0 0 N N N -20.176 57.555 25.956 -5.628 3.381 -1.323 HN2A GX1 30 GX1 HN4 HN4 H 0 1 N N N -12.701 53.196 30.192 5.139 -0.657 1.223 HN4 GX1 31 GX1 H8 H8 H 0 1 N N N -18.082 50.676 28.188 -1.886 -2.198 0.828 H8 GX1 32 GX1 "H1'" "H1'" H 0 1 N N N -18.025 51.628 24.933 -1.487 1.299 -0.611 "H1'" GX1 33 GX1 "H2'" "H2'" H 0 1 N N N -16.561 53.404 24.298 -1.655 2.287 1.510 "H2'" GX1 34 GX1 "H2'A" "H2'A" H 0 0 N N N -16.605 53.992 25.973 -1.803 0.705 2.338 "H2'A" GX1 35 GX1 "H3'" "H3'" H 0 1 N N N -14.284 53.312 25.945 0.475 0.687 2.712 "H3'" GX1 36 GX1 "HO3'" "HO3'" H 0 0 N Y N -13.642 51.713 24.453 0.365 3.095 2.638 "HO3'" GX1 37 GX1 "H4'" "H4'" H 0 1 N N N -14.339 50.787 26.603 1.129 1.281 -0.180 "H4'" GX1 38 GX1 "H5'" "H5'" H 0 1 N N N -16.344 52.659 27.892 2.743 0.255 1.492 "H5'" GX1 39 GX1 "H5'A" "H5'A" H 0 0 N N N -15.984 50.995 28.511 1.655 -1.149 1.600 "H5'A" GX1 40 GX1 "H7'" "H7'" H 0 1 N N N -11.972 52.976 32.501 6.363 -0.186 -1.288 "H7'" GX1 41 GX1 "H7'A" "H7'A" H 0 0 N N N -13.492 52.040 32.725 4.638 0.251 -1.289 "H7'A" GX1 42 GX1 "H8'" "H8'" H 0 1 N N N -12.795 50.307 31.373 6.712 1.191 0.744 "H8'" GX1 43 GX1 "H8'A" "H8'A" H 0 0 N N N -11.205 50.850 32.047 4.986 1.628 0.743 "H8'A" GX1 44 GX1 HOP1 HOP1 H 0 0 N N N -16.167 51.501 31.066 4.275 -1.849 -2.333 HOP1 GX1 45 # 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 GX1 OP2 P DOUB N N 1 GX1 "O5'" P SING N N 2 GX1 P OP1 SING N N 3 GX1 P N4 SING N N 4 GX1 S "C8'" SING N N 5 GX1 S HS SING N N 6 GX1 C2 N1 SING N N 7 GX1 N1 C6 SING N N 8 GX1 N1 HN1 SING N N 9 GX1 N2 C2 SING N N 10 GX1 N3 C2 DOUB N N 11 GX1 N2 HN2 SING N N 12 GX1 N2 HN2A SING N N 13 GX1 N3 C4 SING N N 14 GX1 N9 C4 SING Y N 15 GX1 C4 C5 DOUB Y N 16 GX1 N4 "C7'" SING N N 17 GX1 N4 HN4 SING N N 18 GX1 C5 C6 SING N N 19 GX1 C5 N7 SING Y N 20 GX1 C6 O6 DOUB N N 21 GX1 C8 N7 DOUB Y N 22 GX1 N9 C8 SING Y N 23 GX1 C8 H8 SING N N 24 GX1 "C1'" N9 SING N N 25 GX1 "C2'" "C1'" SING N N 26 GX1 "C1'" "O4'" SING N N 27 GX1 "C1'" "H1'" SING N N 28 GX1 "C2'" "C3'" SING N N 29 GX1 "C2'" "H2'" SING N N 30 GX1 "C2'" "H2'A" SING N N 31 GX1 "O3'" "C3'" SING N N 32 GX1 "C3'" "C4'" SING N N 33 GX1 "C3'" "H3'" SING N N 34 GX1 "O3'" "HO3'" SING N N 35 GX1 "O4'" "C4'" SING N N 36 GX1 "C4'" "C5'" SING N N 37 GX1 "C4'" "H4'" SING N N 38 GX1 "C5'" "O5'" SING N N 39 GX1 "C5'" "H5'" SING N N 40 GX1 "C5'" "H5'A" SING N N 41 GX1 "C8'" "C7'" SING N N 42 GX1 "C7'" "H7'" SING N N 43 GX1 "C7'" "H7'A" SING N N 44 GX1 "C8'" "H8'" SING N N 45 GX1 "C8'" "H8'A" SING N N 46 GX1 OP1 HOP1 SING N N 47 # 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 GX1 SMILES ACDLabs 11.02 "O=P(O)(OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O)NCCS" GX1 SMILES_CANONICAL CACTVS 3.352 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O3" GX1 SMILES CACTVS 3.352 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)NCCS)O3" GX1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(NCCS)O)O)N=C(NC2=O)N" GX1 SMILES "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(NCCS)O)O)N=C(NC2=O)N" GX1 InChI InChI 1.03 "InChI=1S/C12H19N6O6PS/c13-12-16-10-9(11(20)17-12)14-5-18(10)8-3-6(19)7(24-8)4-23-25(21,22)15-1-2-26/h5-8,19,26H,1-4H2,(H2,15,21,22)(H3,13,16,17,20)/t6-,7+,8+/m0/s1" GX1 InChIKey InChI 1.03 VONCJIFEOZVCEV-XLPZGREQSA-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 GX1 "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}guanosine" GX1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-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 GX1 "Create component" 2009-09-09 RCSB GX1 "Modify aromatic_flag" 2011-06-04 RCSB GX1 "Modify descriptor" 2011-06-04 RCSB #