data_VPG
#

_chem_comp.id                                   VPG
_chem_comp.name                                 "6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H20 Cl2 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ADN
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-08-31
_chem_comp.pdbx_modified_date                   2020-09-18
_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                       520.260
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VPG
_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       7JV9
_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
VPG  C2    C1   C   0  1  Y  N  N  30.637  -20.150   2.868   6.403   1.617   0.880  C2    VPG   1  
VPG  C3    C2   C   0  1  Y  N  N  30.418  -19.101   3.751   7.176   2.730   1.161  C3    VPG   2  
VPG  C4    C3   C   0  1  Y  N  N  30.958  -19.138   5.028   7.497   3.620   0.154  C4    VPG   3  
VPG  C5    C4   C   0  1  Y  N  N  31.736  -20.217   5.430   7.046   3.399  -1.135  C5    VPG   4  
VPG  C6    C5   C   0  1  Y  N  N  31.969  -21.263   4.552   6.273   2.288  -1.416  C6    VPG   5  
VPG  C7    C6   C   0  1  Y  N  N  31.424  -21.237   3.265   5.952   1.396  -0.409  C7    VPG   6  
VPG  C8    C7   C   0  1  N  N  N  31.713  -22.403   2.346   5.110   0.185  -0.716  C8    VPG   7  
VPG  C12   C8   C   0  1  Y  N  N  35.436  -23.414  -0.606   2.164  -2.649  -1.210  C12   VPG   8  
VPG  C15   C9   C   0  1  Y  N  N  33.655  -24.884  -0.828   0.488  -1.340  -0.331  C15   VPG   9  
VPG  C16   C10  C   0  1  Y  N  N  32.984  -24.218   0.228   1.426  -0.310  -0.118  C16   VPG  10  
VPG  C17   C11  C   0  1  Y  N  N  31.755  -24.896   0.402   0.728   0.771   0.462  C17   VPG  11  
VPG  C23   C12  C   0  1  N  N  N  29.907  -28.593  -2.375  -5.396  -0.352   0.339  C23   VPG  12  
VPG  O28   O1   O   0  1  N  N  N  26.575  -27.705  -5.499  -5.635   2.534   1.009  O28   VPG  13  
VPG  O29   O2   O   0  1  N  N  N  25.632  -26.504  -3.271  -5.011   3.192  -1.346  O29   VPG  14  
VPG  C30   C13  C   0  1  N  N  S  32.142  -29.044  -1.567  -3.877  -1.934   1.589  C30   VPG  15  
VPG  C32   C14  C   0  1  N  N  R  33.438  -28.197  -1.577  -2.342  -2.092   1.518  C32   VPG  16  
VPG  CL1   CL1  CL  0  0  N  N  N  29.930  -20.050   1.285   6.005   0.495   2.143  CL1   VPG  17  
VPG  N9    N1   N   0  1  N  N  N  33.110  -22.355   1.884   3.724   0.438  -0.314  N9    VPG  18  
VPG  C10   C15  C   0  1  Y  N  N  33.627  -23.111   0.833   2.763  -0.536  -0.499  C10   VPG  19  
VPG  N11   N2   N   0  1  Y  N  N  34.834  -22.773   0.376   3.079  -1.712  -1.030  N11   VPG  20  
VPG  CL13  CL2  CL  0  0  N  N  N  37.015  -22.841  -1.084   2.648  -4.163  -1.910  CL13  VPG  21  
VPG  N14   N3   N   0  1  Y  N  N  34.862  -24.449  -1.209   0.902  -2.483  -0.875  N14   VPG  22  
VPG  N18   N4   N   0  1  Y  N  N  31.682  -25.868  -0.441  -0.523   0.432   0.593  N18   VPG  23  
VPG  N19   N5   N   0  1  Y  N  N  32.822  -25.893  -1.218  -0.711  -0.872   0.118  N19   VPG  24  
VPG  C20   C16  C   0  1  N  N  R  33.007  -26.873  -2.247  -1.980  -1.604   0.098  C20   VPG  25  
VPG  O21   O3   O   0  1  N  N  N  31.714  -27.080  -2.848  -3.062  -0.724  -0.277  O21   VPG  26  
VPG  C22   C17  C   0  1  N  N  R  31.362  -28.458  -2.736  -4.261  -1.369   0.204  C22   VPG  27  
VPG  O24   O4   O   0  1  N  N  N  29.128  -28.243  -3.503  -5.764   0.126  -0.957  O24   VPG  28  
VPG  C25   C18  C   0  1  N  N  N  27.739  -28.366  -3.199  -6.821   1.087  -0.943  C25   VPG  29  
VPG  P26   P1   P   0  1  N  N  N  26.919  -27.035  -4.077  -6.179   2.690  -0.359  P26   VPG  30  
VPG  O27   O5   O   0  1  N  N  N  27.807  -25.873  -4.277  -7.371   3.772  -0.343  O27   VPG  31  
VPG  O31   O6   O   0  1  N  N  N  32.375  -30.441  -1.801  -4.502  -3.201   1.807  O31   VPG  32  
VPG  O33   O7   O   0  1  N  N  N  34.478  -28.811  -2.344  -1.971  -3.461   1.690  O33   VPG  33  
VPG  H1    H1   H   0  1  N  N  N  29.825  -18.253   3.442   7.528   2.903   2.167  H1    VPG  34  
VPG  H2    H2   H   0  1  N  N  N  30.773  -18.324   5.713   8.101   4.488   0.373  H2    VPG  35  
VPG  H3    H3   H   0  1  N  N  N  32.158  -20.240   6.424   7.297   4.095  -1.921  H3    VPG  36  
VPG  H4    H4   H   0  1  N  N  N  32.574  -22.102   4.863   5.920   2.116  -2.422  H4    VPG  37  
VPG  H5    H5   H   0  1  N  N  N  31.041  -22.355   1.476   5.146  -0.021  -1.786  H5    VPG  38  
VPG  H6    H6   H   0  1  N  N  N  31.543  -23.344   2.889   5.497  -0.674  -0.168  H6    VPG  39  
VPG  H7    H7   H   0  1  N  N  N  30.997  -24.639   1.127   1.158   1.719   0.750  H7    VPG  40  
VPG  H8    H8   H   0  1  N  N  N  29.669  -27.921  -1.537  -6.256  -0.828   0.808  H8    VPG  41  
VPG  H9    H9   H   0  1  N  N  N  29.692  -29.632  -2.084  -5.062   0.484   0.953  H9    VPG  42  
VPG  H10   H10  H   0  1  N  N  N  24.847  -26.675  -3.778  -5.296   3.315  -2.262  H10   VPG  43  
VPG  H11   H11  H   0  1  N  N  N  31.596  -28.879  -0.626  -4.153  -1.233   2.377  H11   VPG  44  
VPG  H12   H12  H   0  1  N  N  N  33.762  -28.003  -0.544  -1.859  -1.469   2.271  H12   VPG  45  
VPG  H13   H13  H   0  1  N  N  N  33.664  -22.592   2.682   3.483   1.290   0.082  H13   VPG  46  
VPG  H14   H14  H   0  1  N  N  N  33.757  -26.557  -2.987  -1.919  -2.448  -0.589  H14   VPG  47  
VPG  H15   H15  H   0  1  N  N  N  31.584  -29.012  -3.660  -4.554  -2.175  -0.469  H15   VPG  48  
VPG  H16   H16  H   0  1  N  N  N  27.575  -28.267  -2.116  -7.222   1.201  -1.950  H16   VPG  49  
VPG  H17   H17  H   0  1  N  N  N  27.358  -29.340  -3.540  -7.612   0.747  -0.274  H17   VPG  50  
VPG  H18   H18  H   0  1  N  N  N  27.987  -25.767  -5.204  -7.100   4.650  -0.042  H18   VPG  51  
VPG  H19   H19  H   0  1  N  N  N  32.862  -30.808  -1.072  -4.270  -3.614   2.650  H19   VPG  52  
VPG  H20   H20  H   0  1  N  N  N  34.740  -29.624  -1.929  -2.229  -3.835   2.543  H20   VPG  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
VPG  O28   P26  DOUB  N  N   1  
VPG  O27   P26  SING  N  N   2  
VPG  P26   O29  SING  N  N   3  
VPG  P26   C25  SING  N  N   4  
VPG  O24   C25  SING  N  N   5  
VPG  O24   C23  SING  N  N   6  
VPG  O21   C22  SING  N  N   7  
VPG  O21   C20  SING  N  N   8  
VPG  C22   C23  SING  N  N   9  
VPG  C22   C30  SING  N  N  10  
VPG  O33   C32  SING  N  N  11  
VPG  C20   C32  SING  N  N  12  
VPG  C20   N19  SING  N  N  13  
VPG  O31   C30  SING  N  N  14  
VPG  C32   C30  SING  N  N  15  
VPG  N19   C15  SING  Y  N  16  
VPG  N19   N18  SING  Y  N  17  
VPG  N14   C15  DOUB  Y  N  18  
VPG  N14   C12  SING  Y  N  19  
VPG  CL13  C12  SING  N  N  20  
VPG  C15   C16  SING  Y  N  21  
VPG  C12   N11  DOUB  Y  N  22  
VPG  N18   C17  DOUB  Y  N  23  
VPG  C16   C17  SING  Y  N  24  
VPG  C16   C10  DOUB  Y  N  25  
VPG  N11   C10  SING  Y  N  26  
VPG  C10   N9   SING  N  N  27  
VPG  CL1   C2   SING  N  N  28  
VPG  N9    C8   SING  N  N  29  
VPG  C8    C7   SING  N  N  30  
VPG  C2    C7   DOUB  Y  N  31  
VPG  C2    C3   SING  Y  N  32  
VPG  C7    C6   SING  Y  N  33  
VPG  C3    C4   DOUB  Y  N  34  
VPG  C6    C5   DOUB  Y  N  35  
VPG  C4    C5   SING  Y  N  36  
VPG  C3    H1   SING  N  N  37  
VPG  C4    H2   SING  N  N  38  
VPG  C5    H3   SING  N  N  39  
VPG  C6    H4   SING  N  N  40  
VPG  C8    H5   SING  N  N  41  
VPG  C8    H6   SING  N  N  42  
VPG  C17   H7   SING  N  N  43  
VPG  C23   H8   SING  N  N  44  
VPG  C23   H9   SING  N  N  45  
VPG  O29   H10  SING  N  N  46  
VPG  C30   H11  SING  N  N  47  
VPG  C32   H12  SING  N  N  48  
VPG  N9    H13  SING  N  N  49  
VPG  C20   H14  SING  N  N  50  
VPG  C22   H15  SING  N  N  51  
VPG  C25   H16  SING  N  N  52  
VPG  C25   H17  SING  N  N  53  
VPG  O27   H18  SING  N  N  54  
VPG  O31   H19  SING  N  N  55  
VPG  O33   H20  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
VPG  SMILES            ACDLabs               12.01  "c1(c(cccc1)CNc2c3c(nc(n2)Cl)n(nc3)C4C(C(C(COCP(=O)(O)O)O4)O)O)Cl"  
VPG  InChI             InChI                 1.03   "InChI=1S/C18H20Cl2N5O7P/c19-11-4-2-1-3-9(11)5-21-15-10-6-22-25(16(10)24-18(20)23-15)17-14(27)13(26)12(32-17)7-31-8-33(28,29)30/h1-4,6,12-14,17,26-27H,5,7-8H2,(H,21,23,24)(H2,28,29,30)/t12-,13-,14-,17-/m1/s1"  
VPG  InChIKey          InChI                 1.03   VAGWGCSOWAKFTM-VMUDFCTBSA-N  
VPG  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COC[P](O)(O)=O)n2ncc3c(NCc4ccccc4Cl)nc(Cl)nc23"  
VPG  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1COC[P](O)(O)=O)n2ncc3c(NCc4ccccc4Cl)nc(Cl)nc23"  
VPG  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(c(c1)CNc2c3cnn(c3nc(n2)Cl)[C@H]4[C@@H]([C@@H]([C@H](O4)COCP(=O)(O)O)O)O)Cl"  
VPG  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(c(c1)CNc2c3cnn(c3nc(n2)Cl)C4C(C(C(O4)COCP(=O)(O)O)O)O)Cl"  
#   #
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
VPG  "SYSTEMATIC NAME"  ACDLabs               12.01  "6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine"  
VPG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[(2-chlorophenyl)methylamino]pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic 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
VPG  "Create component"  2020-09-01  RCSB  
VPG  "Initial release"   2020-09-23  RCSB  
##
