data_V2P
#

_chem_comp.id                                   V2P
_chem_comp.name                                 "(2~{S})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]pyrrolidine-2-carboxylic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H21 N6 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-06-19
_chem_comp.pdbx_modified_date                   2021-03-12
_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                       444.336
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    V2P
_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       6XHD
_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
V2P  C      C1   C  0  1  N  N  N  39.040   2.009  12.205   5.404   2.173   0.424  C      V2P   1  
V2P  N      N1   N  0  1  N  N  N  36.704   1.998  11.351   3.711   0.502  -0.122  N      V2P   2  
V2P  O      O1   O  0  1  N  N  N  39.414   2.482  11.100   4.499   2.778   0.948  O      V2P   3  
V2P  C2     C2   C  0  1  Y  N  N  38.689   2.247  17.308  -6.589   0.266   1.010  C2     V2P   4  
V2P  C4     C3   C  0  1  Y  N  N  37.369   4.212  17.472  -4.406   0.450   0.315  C4     V2P   5  
V2P  C5     C4   C  0  1  Y  N  N  36.662   3.716  18.503  -4.677   1.743  -0.161  C5     V2P   6  
V2P  C6     C5   C  0  1  Y  N  N  36.941   2.511  18.948  -5.979   2.249  -0.003  C6     V2P   7  
V2P  C8     C6   C  0  1  Y  N  N  35.901   5.663  18.081  -2.591   1.326  -0.581  C8     V2P   8  
V2P  N9     N2   N  0  1  Y  N  N  36.890   5.418  17.220  -3.083   0.214   0.036  N9     V2P   9  
V2P  CA     C7   C  0  1  N  N  S  37.658   1.309  12.245   5.139   0.849  -0.244  CA     V2P  10  
V2P  CB     C8   C  0  1  N  N  N  37.726  -0.145  11.679   5.458   0.947  -1.751  CB     V2P  11  
V2P  CG     C9   C  0  1  N  N  N  36.385  -0.333  10.941   4.068   1.210  -2.386  CG     V2P  12  
V2P  OXT    O2   O  0  1  N  N  N  39.653   2.132  13.297   6.646   2.684   0.433  OXT    V2P  13  
V2P  CD     C10  C  0  1  N  N  N  36.084   1.060  10.389   3.144   0.359  -1.479  CD     V2P  14  
V2P  PA     P1   P  0  1  N  N  N  36.098   3.441  11.609   3.508  -0.912   0.769  PA     V2P  15  
V2P  O1A    O3   O  0  1  N  N  N  36.688   4.239  10.507   4.211  -2.026   0.093  O1A    V2P  16  
V2P  O2A    O4   O  0  1  N  N  N  34.649   3.224  11.729   4.119  -0.709   2.245  O2A    V2P  17  
V2P  "O5'"  O5   O  0  1  N  N  N  36.609   4.188  12.900   1.939  -1.255   0.879  "O5'"  V2P  18  
V2P  "C5'"  C11  C  0  1  N  N  N  36.182   5.568  12.860   1.181  -1.791  -0.207  "C5'"  V2P  19  
V2P  "C4'"  C12  C  0  1  N  N  R  37.002   6.525  13.745  -0.268  -1.999   0.236  "C4'"  V2P  20  
V2P  "O4'"  O6   O  0  1  N  N  N  36.450   6.646  15.111  -0.922  -0.725   0.428  "O4'"  V2P  21  
V2P  "C3'"  C13  C  0  1  N  N  S  38.444   6.051  13.853  -1.078  -2.693  -0.882  "C3'"  V2P  22  
V2P  "O3'"  O7   O  0  1  N  N  N  39.340   7.192  13.860  -1.180  -4.096  -0.628  "O3'"  V2P  23  
V2P  "C2'"  C14  C  0  1  N  N  R  38.451   5.371  15.202  -2.469  -2.026  -0.807  "C2'"  V2P  24  
V2P  "O2'"  O8   O  0  1  N  N  N  39.791   5.357  15.736  -3.474  -2.997  -0.505  "O2'"  V2P  25  
V2P  "C1'"  C15  C  0  1  N  N  R  37.474   6.235  16.067  -2.336  -1.008   0.346  "C1'"  V2P  26  
V2P  N7     N3   N  0  1  Y  N  N  35.770   4.605  18.891  -3.528   2.221  -0.696  N7     V2P  27  
V2P  N3     N4   N  0  1  Y  N  N  38.365   3.524  16.862  -5.383  -0.246   0.888  N3     V2P  28  
V2P  N1     N5   N  0  1  Y  N  N  37.919   1.769  18.374  -6.891   1.477   0.578  N1     V2P  29  
V2P  N6     N6   N  0  1  N  N  N  36.189   2.095  19.963  -6.306   3.516  -0.452  N6     V2P  30  
V2P  H1     H1   H  0  1  N  N  N  39.481   1.664  16.862  -7.361  -0.327   1.476  H1     V2P  31  
V2P  H2     H2   H  0  1  N  N  N  35.306   6.563  18.118  -1.574   1.445  -0.924  H2     V2P  32  
V2P  H3     H3   H  0  1  N  N  N  37.280   1.287  13.278   5.750   0.072   0.217  H3     V2P  33  
V2P  H4     H4   H  0  1  N  N  N  37.827  -0.876  12.495   6.135   1.779  -1.948  H4     V2P  34  
V2P  H5     H5   H  0  1  N  N  N  38.571  -0.253  10.984   5.882   0.012  -2.117  H5     V2P  35  
V2P  H6     H6   H  0  1  N  N  N  35.597  -0.660  11.635   3.805   2.267  -2.329  H6     V2P  36  
V2P  H7     H7   H  0  1  N  N  N  36.484  -1.066  10.127   4.036   0.858  -3.417  H7     V2P  37  
V2P  H8     H8   H  0  1  N  N  N  40.445   2.639  13.161   6.766   3.537   0.873  H8     V2P  38  
V2P  H9     H9   H  0  1  N  N  N  36.527   1.183   9.390   3.163  -0.685  -1.791  H9     V2P  39  
V2P  H10    H10  H  0  1  N  N  N  34.998   1.227  10.332   2.125   0.745  -1.507  H10    V2P  40  
V2P  H11    H11  H  0  1  N  N  N  34.202   3.663  11.015   3.705   0.007   2.747  H11    V2P  41  
V2P  H12    H12  H  0  1  N  N  N  36.254   5.918  11.820   1.209  -1.097  -1.047  H12    V2P  42  
V2P  H13    H13  H  0  1  N  N  N  35.133   5.611  13.190   1.609  -2.747  -0.511  H13    V2P  43  
V2P  H14    H14  H  0  1  N  N  N  36.999   7.517  13.270  -0.304  -2.588   1.152  H14    V2P  44  
V2P  H15    H15  H  0  1  N  N  N  38.686   5.340  13.049  -0.618  -2.515  -1.854  H15    V2P  45  
V2P  H16    H16  H  0  1  N  N  N  40.238   6.890  13.928  -1.679  -4.582  -1.299  H16    V2P  46  
V2P  H17    H17  H  0  1  N  N  N  38.051   4.350  15.112  -2.700  -1.518  -1.744  H17    V2P  47  
V2P  H18    H18  H  0  1  N  N  N  39.790   4.929  16.584  -3.559  -3.695  -1.168  H18    V2P  48  
V2P  H19    H19  H  0  1  N  N  N  38.013   7.108  16.463  -2.691  -1.443   1.280  H19    V2P  49  
V2P  H20    H20  H  0  1  N  N  N  36.461   1.168  20.222  -5.633   4.067  -0.882  H20    V2P  50  
V2P  H21    H21  H  0  1  N  N  N  36.312   2.709  20.743  -7.208   3.854  -0.338  H21    V2P  51  
#   #
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
V2P  CD     CG     SING  N  N   1  
V2P  CD     N      SING  N  N   2  
V2P  O1A    PA     DOUB  N  N   3  
V2P  CG     CB     SING  N  N   4  
V2P  O      C      DOUB  N  N   5  
V2P  N      PA     SING  N  N   6  
V2P  N      CA     SING  N  N   7  
V2P  PA     O2A    SING  N  N   8  
V2P  PA     "O5'"  SING  N  N   9  
V2P  CB     CA     SING  N  N  10  
V2P  C      CA     SING  N  N  11  
V2P  C      OXT    SING  N  N  12  
V2P  "C5'"  "O5'"  SING  N  N  13  
V2P  "C5'"  "C4'"  SING  N  N  14  
V2P  "C4'"  "C3'"  SING  N  N  15  
V2P  "C4'"  "O4'"  SING  N  N  16  
V2P  "C3'"  "O3'"  SING  N  N  17  
V2P  "C3'"  "C2'"  SING  N  N  18  
V2P  "O4'"  "C1'"  SING  N  N  19  
V2P  "C2'"  "O2'"  SING  N  N  20  
V2P  "C2'"  "C1'"  SING  N  N  21  
V2P  "C1'"  N9     SING  N  N  22  
V2P  N3     C2     DOUB  Y  N  23  
V2P  N3     C4     SING  Y  N  24  
V2P  N9     C4     SING  Y  N  25  
V2P  N9     C8     SING  Y  N  26  
V2P  C2     N1     SING  Y  N  27  
V2P  C4     C5     DOUB  Y  N  28  
V2P  C8     N7     DOUB  Y  N  29  
V2P  N1     C6     DOUB  Y  N  30  
V2P  C5     N7     SING  Y  N  31  
V2P  C5     C6     SING  Y  N  32  
V2P  C6     N6     SING  N  N  33  
V2P  C2     H1     SING  N  N  34  
V2P  C8     H2     SING  N  N  35  
V2P  CA     H3     SING  N  N  36  
V2P  CB     H4     SING  N  N  37  
V2P  CB     H5     SING  N  N  38  
V2P  CG     H6     SING  N  N  39  
V2P  CG     H7     SING  N  N  40  
V2P  OXT    H8     SING  N  N  41  
V2P  CD     H9     SING  N  N  42  
V2P  CD     H10    SING  N  N  43  
V2P  O2A    H11    SING  N  N  44  
V2P  "C5'"  H12    SING  N  N  45  
V2P  "C5'"  H13    SING  N  N  46  
V2P  "C4'"  H14    SING  N  N  47  
V2P  "C3'"  H15    SING  N  N  48  
V2P  "O3'"  H16    SING  N  N  49  
V2P  "C2'"  H17    SING  N  N  50  
V2P  "O2'"  H18    SING  N  N  51  
V2P  "C1'"  H19    SING  N  N  52  
V2P  N6     H20    SING  N  N  53  
V2P  N6     H21    SING  N  N  54  
#   #
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
V2P  SMILES            ACDLabs               12.01  "C(C4N(P(O)(OCC3C(O)C(O)C(n1c2c(nc1)c(N)ncn2)O3)=O)CCC4)(O)=O"  
V2P  InChI             InChI                 1.03   "InChI=1S/C15H21N6O8P/c16-12-9-13(18-5-17-12)20(6-19-9)14-11(23)10(22)8(29-14)4-28-30(26,27)21-3-1-2-7(21)15(24)25/h5-8,10-11,14,22-23H,1-4H2,(H,24,25)(H,26,27)(H2,16,17,18)/t7-,8+,10+,11+,14+/m0/s1"  
V2P  InChIKey          InChI                 1.03   YHPWCYBNNLQQNG-TWBCTODHSA-N  
V2P  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N4CCC[C@H]4C(O)=O)[C@@H](O)[C@H]3O"  
V2P  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N4CCC[CH]4C(O)=O)[CH](O)[CH]3O"  
V2P  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N4CCC[C@H]4C(=O)O)O)O)O)N"  
V2P  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N4CCCC4C(=O)O)O)O)O)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
V2P  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S)-1-[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]pyrrolidine-2-carboxylic acid (non-preferred name)"  
V2P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]pyrrolidine-2-carboxylic 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
V2P  "Create component"  2020-06-19  RCSB  
V2P  "Initial release"   2021-03-17  RCSB  
##
