data_6WI
#

_chem_comp.id                                   6WI
_chem_comp.name                                 "3-(guanosine-5'-diphospho)-D-glycerate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H19 N5 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "3GPPG; (2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-08-04
_chem_comp.pdbx_modified_date                   2022-01-28
_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                       531.263
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    6WI
_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       7P97
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
6WI  C4      C4     C  0  1  Y  N  N  -13.857  22.993  34.352   5.075  -1.180   0.059  C4      6WI   1  
6WI  C5      C5     C  0  1  Y  N  N  -12.847  22.703  33.441   5.087  -2.219  -0.878  C5      6WI   2  
6WI  C6      C6     C  0  1  N  N  N  -12.048  23.684  33.006   6.193  -3.102  -0.895  C6      6WI   3  
6WI  C8      C8     C  0  1  Y  N  N  -13.896  20.860  33.884   3.246  -1.113  -1.170  C8      6WI   4  
6WI  N1      N1     N  0  1  N  N  N  -12.272  24.950  33.539   7.189  -2.900  -0.004  N1      6WI   5  
6WI  N2      N2     N  0  1  N  N  N  -13.462  26.456  34.834   8.145  -1.689   1.778  N2      6WI   6  
6WI  N3      N3     N  0  1  N  N  N  -14.082  24.234  34.807   6.100  -1.039   0.907  N3      6WI   7  
6WI  OBF     OBF    O  0  1  N  N  N  -13.792  13.144  40.675  -8.403  -3.403   1.299  OBF     6WI   8  
6WI  CBD     CBD    C  0  1  N  N  N  -13.114  14.233  40.588  -7.438  -3.306   0.579  CBD     6WI   9  
6WI  OBG     OBG    O  0  1  N  N  N  -11.855  14.384  40.732  -7.397  -3.978  -0.582  OBG     6WI  10  
6WI  CBC     CBC    C  0  1  N  N  R  -13.875  15.492  40.255  -6.280  -2.431   0.984  CBC     6WI  11  
6WI  OBD     OBD    O  0  1  N  N  N  -15.221  15.252  40.516  -6.507  -1.919   2.299  OBD     6WI  12  
6WI  CBE     CBE    C  0  1  N  N  N  -13.774  15.807  38.751  -6.151  -1.266   0.000  CBE     6WI  13  
6WI  O3B     OAT    O  0  1  N  N  N  -13.900  14.618  37.968  -4.985  -0.503   0.315  O3B     6WI  14  
6WI  PB      PAQ    P  0  1  N  N  N  -14.958  14.492  36.826  -4.539   0.800  -0.518  PB      6WI  15  
6WI  O2B     OAS    O  0  1  N  N  N  -16.255  14.049  37.557  -5.645   1.956  -0.340  O2B     6WI  16  
6WI  O1B     OAR    O  0  1  N  N  N  -14.462  13.461  35.888  -4.416   0.451  -1.951  O1B     6WI  17  
6WI  O3A     OAP    O  0  1  N  N  N  -14.963  15.952  36.236  -3.119   1.327   0.030  O3A     6WI  18  
6WI  PA      PAM    P  0  1  N  N  N  -16.142  16.556  35.313  -2.012   2.349  -0.537  PA      6WI  19  
6WI  O2A     OAO    O  0  1  N  N  N  -17.485  16.242  35.949  -2.478   3.862  -0.245  O2A     6WI  20  
6WI  O1A     OAN    O  0  1  N  N  N  -16.040  16.358  33.873  -1.860   2.153  -1.996  O1A     6WI  21  
6WI  "O5'"   "O5'"  O  0  1  N  N  N  -15.881  18.184  35.579  -0.603   2.072   0.192  "O5'"   6WI  22  
6WI  "C5'"   "C5'"  C  0  1  N  N  N  -16.194  18.622  36.961   0.605   2.746  -0.167  "C5'"   6WI  23  
6WI  "C4'"   "C4'"  C  0  1  N  N  R  -16.312  20.145  37.090   1.749   2.248   0.719  "C4'"   6WI  24  
6WI  "O4'"   "O4'"  O  0  1  N  N  N  -15.146  20.880  36.633   2.028   0.869   0.427  "O4'"   6WI  25  
6WI  "C3'"   "C3'"  C  0  1  N  N  S  -17.525  20.570  36.258   3.030   3.052   0.421  "C3'"   6WI  26  
6WI  "O3'"   "O3'"  O  0  1  N  N  N  -18.325  21.603  36.965   3.480   3.728   1.596  "O3'"   6WI  27  
6WI  "C2'"   "C2'"  C  0  1  N  N  R  -16.835  21.025  35.015   4.057   1.979  -0.014  "C2'"   6WI  28  
6WI  "O2'"   "O2'"  O  0  1  N  N  N  -17.656  21.952  34.302   5.345   2.248   0.544  "O2'"   6WI  29  
6WI  "C1'"   "C1'"  C  0  1  N  N  R  -15.596  21.724  35.579   3.451   0.683   0.592  "C1'"   6WI  30  
6WI  N9      N9     N  0  1  Y  N  N  -14.494  21.838  34.627   3.907  -0.496  -0.148  N9      6WI  31  
6WI  C2      C2     C  0  1  N  N  N  -13.284  25.209  34.433   7.119  -1.869   0.885  C2      6WI  32  
6WI  O6      O6     O  0  1  N  N  N  -11.104  23.513  32.211   6.245  -4.021  -1.694  O6      6WI  33  
6WI  N7      N7     N  0  1  Y  N  N  -12.876  21.357  33.172   3.945  -2.123  -1.601  N7      6WI  34  
6WI  H8      H8     H  0  1  N  N  N  -14.204  19.825  33.872   2.290  -0.806  -1.567  H8      6WI  35  
6WI  HN1     H1     H  0  1  N  N  N  -11.673  25.701  33.261   7.957  -3.492   0.003  HN1     6WI  36  
6WI  HN21    H22    H  0  0  N  N  N  -14.223  26.682  35.442   8.905  -2.291   1.771  HN21    6WI  37  
6WI  HN22    H21    H  0  0  N  N  N  -12.835  27.173  34.530   8.109  -0.960   2.417  HN22    6WI  38  
6WI  HBG     H2     H  0  1  N  N  N  -11.455  13.544  40.923  -8.163  -4.526  -0.800  HBG     6WI  39  
6WI  HBC     HBC    H  0  1  N  N  N  -13.486  16.338  40.840  -5.361  -3.017   0.976  HBC     6WI  40  
6WI  HBD     HBD    H  0  1  N  N  N  -15.348  14.330  40.707  -7.310  -1.387   2.381  HBD     6WI  41  
6WI  HBF     HBF    H  0  1  N  N  N  -12.798  16.271  38.546  -6.067  -1.656  -1.014  HBF     6WI  42  
6WI  HBE     HBE    H  0  1  N  N  N  -14.577  16.506  38.475  -7.033  -0.630   0.073  HBE     6WI  43  
6WI  HOB2    H3     H  0  0  N  N  N  -16.502  13.179  37.265  -5.779   2.235   0.576  HOB2    6WI  44  
6WI  HOA2    H4     H  0  0  N  N  N  -18.092  15.948  35.280  -2.598   4.063   0.693  HOA2    6WI  45  
6WI  "H5''"  "H5'"  H  0  0  N  N  N  -17.149  18.169  37.265   0.839   2.541  -1.212  "H5''"  6WI  46  
6WI  "H5'"   H5V    H  0  1  N  N  N  -15.393  18.274  37.630   0.477   3.819  -0.027  "H5'"   6WI  47  
6WI  "H4'"   "H4'"  H  0  1  N  N  N  -16.510  20.390  38.144   1.479   2.358   1.769  "H4'"   6WI  48  
6WI  "H3'"   "H3'"  H  0  1  N  N  N  -18.149  19.690  36.042   2.854   3.764  -0.385  "H3'"   6WI  49  
6WI  "HO3'"  H8L    H  0  0  N  N  N  -18.723  21.221  37.738   4.284   4.250   1.465  "HO3'"  6WI  50  
6WI  "H2'"   "H2'"  H  0  1  N  N  N  -16.542  20.168  34.390   4.112   1.911  -1.101  "H2'"   6WI  51  
6WI  "HO2'"  H8M    H  0  0  N  N  N  -18.419  21.502  33.960   5.765   3.047   0.197  "HO2'"  6WI  52  
6WI  "H1'"   "H1'"  H  0  1  N  N  N  -15.877  22.716  35.961   3.706   0.597   1.648  "H1'"   6WI  53  
#   #
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
6WI  O6     C6      DOUB  N  N   1  
6WI  C6     C5      SING  N  N   2  
6WI  C6     N1      SING  N  N   3  
6WI  N7     C5      SING  Y  N   4  
6WI  N7     C8      DOUB  Y  N   5  
6WI  C5     C4      DOUB  Y  N   6  
6WI  N1     C2      SING  N  N   7  
6WI  O1A    PA      DOUB  N  N   8  
6WI  C8     N9      SING  Y  N   9  
6WI  "O2'"  "C2'"   SING  N  N  10  
6WI  C4     N9      SING  Y  N  11  
6WI  C4     N3      SING  N  N  12  
6WI  C2     N3      DOUB  N  N  13  
6WI  C2     N2      SING  N  N  14  
6WI  N9     "C1'"   SING  N  N  15  
6WI  "C2'"  "C1'"   SING  N  N  16  
6WI  "C2'"  "C3'"   SING  N  N  17  
6WI  PA     "O5'"   SING  N  N  18  
6WI  PA     O2A     SING  N  N  19  
6WI  PA     O3A     SING  N  N  20  
6WI  "C1'"  "O4'"   SING  N  N  21  
6WI  "O5'"  "C5'"   SING  N  N  22  
6WI  O1B    PB      DOUB  N  N  23  
6WI  O3A    PB      SING  N  N  24  
6WI  "C3'"  "O3'"   SING  N  N  25  
6WI  "C3'"  "C4'"   SING  N  N  26  
6WI  "O4'"  "C4'"   SING  N  N  27  
6WI  PB     O2B     SING  N  N  28  
6WI  PB     O3B     SING  N  N  29  
6WI  "C5'"  "C4'"   SING  N  N  30  
6WI  O3B    CBE     SING  N  N  31  
6WI  CBE    CBC     SING  N  N  32  
6WI  CBC    OBD     SING  N  N  33  
6WI  CBC    CBD     SING  N  N  34  
6WI  CBD    OBF     DOUB  N  N  35  
6WI  CBD    OBG     SING  N  N  36  
6WI  C8     H8      SING  N  N  37  
6WI  N1     HN1     SING  N  N  38  
6WI  N2     HN21    SING  N  N  39  
6WI  N2     HN22    SING  N  N  40  
6WI  OBG    HBG     SING  N  N  41  
6WI  CBC    HBC     SING  N  N  42  
6WI  OBD    HBD     SING  N  N  43  
6WI  CBE    HBF     SING  N  N  44  
6WI  CBE    HBE     SING  N  N  45  
6WI  O2B    HOB2    SING  N  N  46  
6WI  O2A    HOA2    SING  N  N  47  
6WI  "C5'"  "H5''"  SING  N  N  48  
6WI  "C5'"  "H5'"   SING  N  N  49  
6WI  "C4'"  "H4'"   SING  N  N  50  
6WI  "C3'"  "H3'"   SING  N  N  51  
6WI  "O3'"  "HO3'"  SING  N  N  52  
6WI  "C2'"  "H2'"   SING  N  N  53  
6WI  "O2'"  "HO2'"  SING  N  N  54  
6WI  "C1'"  "H1'"   SING  N  N  55  
#   #
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
6WI  InChI             InChI                 1.03   "InChI=1S/C13H19N5O14P2/c14-13-16-9-6(10(22)17-13)15-3-18(9)11-8(21)7(20)5(31-11)2-30-34(27,28)32-33(25,26)29-1-4(19)12(23)24/h3-5,7-8,11,19-21H,1-2H2,(H,23,24)(H,25,26)(H,27,28)(H3,14,16,17,22)/t4-,5-,7-,8-,11-/m1/s1"  
6WI  InChIKey          InChI                 1.03   UBONPDGCIQEDRL-QWEIRQIHSA-N  
6WI  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)C(O)=O)[C@@H](O)[C@H]3O"  
6WI  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)C(O)=O)[CH](O)[CH]3O"  
6WI  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H](C(=O)O)O)O)O)N=C(NC2=O)N"  
6WI  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(=O)O)O)O)O)N=C(NC2=O)N"  
#
_pdbx_chem_comp_identifier.comp_id          6WI
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "(2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid"
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  6WI  3GPPG                                                                                                                                                                                                  AUTHOR  ?  
2  6WI  "(2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid"  PDB     ?  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6WI  "Create component"  2021-08-04  PDBE  
6WI  "Modify atom id"    2021-08-26  PDBE  
6WI  "Initial release"   2022-02-02  RCSB  
##
