data_YPG
#

_chem_comp.id                                   YPG
_chem_comp.name                                 
;[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y
l]-3-oxidanylidene-propyl]phosphonic acid
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H22 N6 O10 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-01-12
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       496.306
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YPG
_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       5HHU
_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
YPG  C4   C1   C  0  1  Y  N  N  31.648   7.033  23.560   2.807  -1.743   0.134  C4   YPG   1  
YPG  C5   C2   C  0  1  Y  N  N  32.177   5.765  23.461   3.700  -2.343  -0.761  C5   YPG   2  
YPG  C6   C3   C  0  1  N  N  N  33.374   5.530  24.135   5.021  -2.603  -0.326  C6   YPG   3  
YPG  C8   C4   C  0  1  Y  N  N  30.360   5.861  22.342   1.810  -2.115  -1.796  C8   YPG   4  
YPG  N1   N1   N  0  1  N  N  N  33.909   6.536  24.811   5.361  -2.260   0.936  N1   YPG   5  
YPG  N2   N2   N  0  1  N  N  N  33.954   8.835  25.618   4.819  -1.341   3.038  N2   YPG   6  
YPG  N3   N3   N  0  1  N  N  N  32.246   7.988  24.254   3.215  -1.431   1.370  N3   YPG   7  
YPG  OAI  O1   O  0  1  N  N  N  25.483   6.622  17.744   3.684   4.492   0.598  OAI  YPG   8  
YPG  PBF  P1   P  0  1  N  N  N  26.846   6.214  18.228   2.992   3.203  -0.074  PBF  YPG   9  
YPG  OAJ  O2   O  0  1  N  N  N  27.635   5.749  17.026   3.828   2.723  -1.197  OAJ  YPG  10  
YPG  OAE  O3   O  0  1  N  N  N  26.731   5.123  19.265   2.848   2.036   1.026  OAE  YPG  11  
YPG  CAZ  C5   C  0  1  N  N  S  27.616   7.681  19.061   1.340   3.657  -0.698  CAZ  YPG  12  
YPG  OAF  O4   O  0  1  N  N  N  27.686   8.789  18.205   0.532   4.121   0.387  OAF  YPG  13  
YPG  CAN  C6   C  0  1  N  N  N  28.998   7.260  19.524   0.682   2.433  -1.336  CAN  YPG  14  
YPG  OAT  O5   O  0  1  N  N  N  29.427   8.188  20.463   0.554   1.397  -0.360  OAT  YPG  15  
YPG  CBA  C7   C  0  1  N  N  R  28.667   8.229  21.699  -0.052   0.202  -0.857  CBA  YPG  16  
YPG  CAO  C8   C  0  1  N  N  N  28.188   9.452  21.878  -1.580   0.236  -0.645  CAO  YPG  17  
YPG  NBC  N4   N  0  1  N  N  N  28.589   9.936  23.358  -1.997  -1.116  -0.245  NBC  YPG  18  
YPG  CAU  C9   C  0  1  N  N  N  28.367  11.277  23.876  -3.255  -1.495   0.052  CAU  YPG  19  
YPG  OAB  O6   O  0  1  N  N  N  28.693  11.552  24.985  -3.484  -2.642   0.370  OAB  YPG  20  
YPG  CAL  C10  C  0  1  N  N  N  27.697  12.326  22.991  -4.379  -0.492  -0.012  CAL  YPG  21  
YPG  CAM  C11  C  0  1  N  N  N  27.699  13.698  23.654  -5.694  -1.175   0.368  CAM  YPG  22  
YPG  PBE  P2   P  0  1  N  N  N  29.424  14.381  23.655  -7.053   0.037   0.291  PBE  YPG  23  
YPG  OAG  O7   O  0  1  N  N  N  29.342  15.828  24.066  -8.413  -0.646   0.817  OAG  YPG  24  
YPG  OAH  O8   O  0  1  N  N  N  29.959  14.292  22.244  -6.724   1.202   1.144  OAH  YPG  25  
YPG  OAD  O9   O  0  1  N  N  N  30.304  13.583  24.591  -7.251   0.525  -1.230  OAD  YPG  26  
YPG  CAP  C12  C  0  1  N  N  N  29.135   8.897  23.974  -0.809  -1.989  -0.224  CAP  YPG  27  
YPG  CBB  C13  C  0  1  N  N  R  29.792   8.238  22.756   0.387  -1.026  -0.017  CBB  YPG  28  
YPG  N9   N5   N  0  1  Y  N  N  30.521   7.060  22.884   1.625  -1.607  -0.543  N9   YPG  29  
YPG  C2   C14  C  0  1  N  N  N  33.359   7.744  24.873   4.445  -1.679   1.761  C2   YPG  30  
YPG  O6   O10  O  0  1  N  N  N  34.002   4.285  24.107   5.832  -3.125  -1.072  O6   YPG  31  
YPG  N7   N6   N  0  1  Y  N  N  31.356   5.047  22.692   3.031  -2.546  -1.921  N7   YPG  32  
YPG  H1   H1   H  0  1  N  N  N  29.535   5.582  21.704   1.056  -2.152  -2.568  H1   YPG  33  
YPG  H2   H2   H  0  1  N  N  N  34.768   6.379  25.298   6.261  -2.429   1.256  H2   YPG  34  
YPG  H3   H3   H  0  1  N  N  N  33.506   9.729  25.639   5.723  -1.518   3.342  H3   YPG  35  
YPG  H4   H4   H  0  1  N  N  N  34.812   8.694  26.111   4.178  -0.927   3.637  H4   YPG  36  
YPG  H5   H5   H  0  1  N  N  N  25.429   6.496  16.804   4.568   4.324   0.952  H5   YPG  37  
YPG  H6   H6   H  0  1  N  N  N  27.182   4.345  18.958   2.312   2.282   1.792  H6   YPG  38  
YPG  H7   H7   H  0  1  N  N  N  26.985   7.895  19.936   1.437   4.448  -1.442  H7   YPG  39  
YPG  H8   H8   H  0  1  N  N  N  28.084   9.519  18.664   0.403   3.468   1.088  H8   YPG  40  
YPG  H9   H9   H  0  1  N  N  N  28.953   6.260  19.979  -0.306   2.704  -1.709  H9   YPG  41  
YPG  H10  H10  H  0  1  N  N  N  29.691   7.243  18.670   1.297   2.079  -2.163  H10  YPG  42  
YPG  H11  H11  H  0  1  N  N  N  27.963   7.394  21.829   0.188   0.058  -1.910  H11  YPG  43  
YPG  H12  H12  H  0  1  N  N  N  28.622  10.135  21.132  -1.830   0.949   0.141  H12  YPG  44  
YPG  H13  H13  H  0  1  N  N  N  27.093   9.442  21.773  -2.077   0.518  -1.574  H13  YPG  45  
YPG  H14  H14  H  0  1  N  N  N  26.657  12.022  22.801  -4.178   0.323   0.683  H14  YPG  46  
YPG  H15  H15  H  0  1  N  N  N  28.241  12.389  22.037  -4.455  -0.096  -1.025  H15  YPG  47  
YPG  H16  H16  H  0  1  N  N  N  27.036  14.376  23.096  -5.894  -1.990  -0.327  H16  YPG  48  
YPG  H17  H17  H  0  1  N  N  N  27.341  13.605  24.690  -5.618  -1.571   1.381  H17  YPG  49  
YPG  H18  H18  H  0  1  N  N  N  29.643  16.378  23.352  -9.179  -0.057   0.804  H18  YPG  50  
YPG  H19  H19  H  0  1  N  N  N  31.014  13.188  24.099  -7.469  -0.187  -1.847  H19  YPG  51  
YPG  H20  H20  H  0  1  N  N  N  28.380   8.247  24.441  -0.873  -2.697   0.602  H20  YPG  52  
YPG  H21  H21  H  0  1  N  N  N  29.874   9.203  24.730  -0.711  -2.520  -1.171  H21  YPG  53  
YPG  H22  H22  H  0  1  N  N  N  30.503   8.993  22.388   0.498  -0.761   1.035  H22  YPG  54  
#   #
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
YPG  OAJ  PBF  DOUB  N  N   1  
YPG  OAI  PBF  SING  N  N   2  
YPG  OAF  CAZ  SING  N  N   3  
YPG  PBF  CAZ  SING  N  N   4  
YPG  PBF  OAE  SING  N  N   5  
YPG  CAZ  CAN  SING  N  N   6  
YPG  CAN  OAT  SING  N  N   7  
YPG  OAT  CBA  SING  N  N   8  
YPG  CBA  CAO  SING  N  N   9  
YPG  CBA  CBB  SING  N  N  10  
YPG  CAO  NBC  SING  N  N  11  
YPG  OAH  PBE  DOUB  N  N  12  
YPG  C8   N7   DOUB  Y  N  13  
YPG  C8   N9   SING  Y  N  14  
YPG  N7   C5   SING  Y  N  15  
YPG  CBB  N9   SING  N  N  16  
YPG  CBB  CAP  SING  N  N  17  
YPG  N9   C4   SING  Y  N  18  
YPG  CAL  CAM  SING  N  N  19  
YPG  CAL  CAU  SING  N  N  20  
YPG  NBC  CAU  SING  N  N  21  
YPG  NBC  CAP  SING  N  N  22  
YPG  C5   C4   DOUB  Y  N  23  
YPG  C5   C6   SING  N  N  24  
YPG  C4   N3   SING  N  N  25  
YPG  CAM  PBE  SING  N  N  26  
YPG  PBE  OAG  SING  N  N  27  
YPG  PBE  OAD  SING  N  N  28  
YPG  CAU  OAB  DOUB  N  N  29  
YPG  O6   C6   DOUB  N  N  30  
YPG  C6   N1   SING  N  N  31  
YPG  N3   C2   DOUB  N  N  32  
YPG  N1   C2   SING  N  N  33  
YPG  C2   N2   SING  N  N  34  
YPG  C8   H1   SING  N  N  35  
YPG  N1   H2   SING  N  N  36  
YPG  N2   H3   SING  N  N  37  
YPG  N2   H4   SING  N  N  38  
YPG  OAI  H5   SING  N  N  39  
YPG  OAE  H6   SING  N  N  40  
YPG  CAZ  H7   SING  N  N  41  
YPG  OAF  H8   SING  N  N  42  
YPG  CAN  H9   SING  N  N  43  
YPG  CAN  H10  SING  N  N  44  
YPG  CBA  H11  SING  N  N  45  
YPG  CAO  H12  SING  N  N  46  
YPG  CAO  H13  SING  N  N  47  
YPG  CAL  H14  SING  N  N  48  
YPG  CAL  H15  SING  N  N  49  
YPG  CAM  H16  SING  N  N  50  
YPG  CAM  H17  SING  N  N  51  
YPG  OAG  H18  SING  N  N  52  
YPG  OAD  H19  SING  N  N  53  
YPG  CAP  H20  SING  N  N  54  
YPG  CAP  H21  SING  N  N  55  
YPG  CBB  H22  SING  N  N  56  
#   #
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
YPG  InChI             InChI                 1.03   "InChI=1S/C14H22N6O10P2/c15-14-17-12-11(13(23)18-14)16-6-20(12)7-3-19(9(21)1-2-31(24,25)26)4-8(7)30-5-10(22)32(27,28)29/h6-8,10,22H,1-5H2,(H2,24,25,26)(H2,27,28,29)(H3,15,17,18,23)/t7-,8-,10+/m1/s1"  
YPG  InChIKey          InChI                 1.03   RBYFDIJTTUISNF-MRTMQBJTSA-N  
YPG  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CN(C[C@H]3OC[C@@H](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O"  
YPG  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3CN(C[CH]3OC[CH](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O"  
YPG  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "c1nc2c(n1[C@@H]3CN(C[C@H]3OC[C@@H](O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N"  
YPG  SMILES            "OpenEye OEToolkits"  2.0.4  "c1nc2c(n1C3CN(CC3OCC(O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N"  
#
_pdbx_chem_comp_identifier.comp_id          YPG
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.4
_pdbx_chem_comp_identifier.identifier       "[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic 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
YPG  "Create component"  2016-01-12  RCSB  
YPG  "Initial release"   2017-01-18  RCSB  
YPG  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     YPG
_pdbx_chem_comp_synonyms.name        "[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
