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                    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                        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 
_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 
GX1 OP2    OP2    O 0 1 N Y N N N 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 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 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 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 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 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 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 N 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 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 N 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 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 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 N 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 N 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 N 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 N N N -17.337 51.939 25.733 -1.445 0.563  0.191  "C1'"  GX1 16 
GX1 "C2'"  "C2'"  C 0 1 N N N 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 N N N -15.005 52.569 25.574 0.241  1.252  1.810  "C3'"  GX1 18 
GX1 "O3'"  "O3'"  O 0 1 N N N 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 N N N -15.241 51.414 26.551 0.821  0.546  0.564  "C4'"  GX1 20 
GX1 "O4'"  "O4'"  O 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 N N 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 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 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 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 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 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 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 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 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 
GX1 "Modify PCM"           2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            GX1 
_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      ? 
# 
