data_VPD
#

_chem_comp.id                                   VPD
_chem_comp.name                                 "6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H29 Cl N5 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ADN
_chem_comp.pdbx_synonyms                        OP-0105244
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-08-31
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       537.888
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VPD
_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       7JV8
_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
VPD  C5    C1   C   0  1  N  N  R  45.920  -28.638  -38.980  -5.083  -0.539   0.735  C5    VPD   1  
VPD  C6    C2   C   0  1  N  N  N  46.729  -27.365  -38.690  -5.486  -1.106   2.098  C6    VPD   2  
VPD  C8    C3   C   0  1  N  N  N  46.856  -29.764  -39.446  -6.196   0.373   0.213  C8    VPD   3  
VPD  O9    O1   O   0  1  N  N  N  47.884  -30.029  -38.500  -7.430  -0.349   0.189  O9    VPD   4  
VPD  C12   C4   C   0  1  N  N  N  44.691  -30.277  -37.598  -3.395   0.765  -0.357  C12   VPD   5  
VPD  C16   C5   C   0  1  N  N  R  41.741  -30.274  -35.485   0.128   1.450  -0.128  C16   VPD   6  
VPD  C21   C6   C   0  1  Y  N  N  38.265  -30.828  -36.274   3.220  -0.486  -0.026  C21   VPD   7  
VPD  C24   C7   C   0  1  N  N  N  35.775  -31.932  -37.694   6.774  -1.669   0.361  C24   VPD   8  
VPD  C27   C8   C   0  1  N  N  N  34.193  -30.453  -38.708   8.829  -2.129  -0.870  C27   VPD   9  
VPD  C30   C9   C   0  1  Y  N  N  37.799  -30.353  -33.621   4.493   1.733   0.790  C30   VPD  10  
VPD  C33   C10  C   0  1  Y  N  N  39.306  -30.520  -35.363   2.525   0.726   0.150  C33   VPD  11  
VPD  C34   C11  C   0  1  N  N  R  42.343  -31.659  -35.148  -0.261   1.889  -1.563  C34   VPD  12  
VPD  C37   C12  C   0  1  N  N  S  43.375  -31.814  -36.252  -1.728   2.348  -1.374  C37   VPD  13  
VPD  O1    O2   O   0  1  N  N  N  45.544  -27.794  -41.457  -3.567  -2.618  -0.094  O1    VPD  14  
VPD  P2    P1   P   0  1  N  N  N  44.734  -28.305  -40.323  -4.818  -1.908  -0.439  P2    VPD  15  
VPD  O3    O3   O   0  1  N  N  N  43.977  -29.640  -40.764  -6.057  -2.933  -0.356  O3    VPD  16  
VPD  O4    O4   O   0  1  N  N  N  43.626  -27.250  -39.864  -4.707  -1.319  -1.933  O4    VPD  17  
VPD  O7    O5   O   0  1  N  N  N  45.872  -26.261  -38.400  -5.806  -0.032   2.985  O7    VPD  18  
VPD  C10   C13  C   0  1  N  N  N  48.783  -31.057  -38.933  -8.540   0.416  -0.286  C10   VPD  19  
VPD  O11   O6   O   0  1  N  N  N  45.181  -28.948  -37.798  -3.876   0.214   0.870  O11   VPD  20  
VPD  C13   C14  C   0  1  N  N  R  43.849  -30.366  -36.349  -2.178   1.650  -0.077  C13   VPD  21  
VPD  O15   O7   O   0  1  N  N  N  42.616  -29.625  -36.426  -1.080   0.841   0.377  O15   VPD  22  
VPD  N18   N1   N   0  1  Y  N  N  40.449  -30.512  -36.077   1.222   0.476  -0.166  N18   VPD  23  
VPD  N19   N2   N   0  1  Y  N  N  40.178  -30.812  -37.404   1.110  -0.871  -0.533  N19   VPD  24  
VPD  C20   C15  C   0  1  Y  N  N  38.900  -30.993  -37.532   2.276  -1.447  -0.449  C20   VPD  25  
VPD  C22   C16  C   0  1  Y  N  N  36.938  -30.882  -35.729   4.603  -0.507   0.238  C22   VPD  26  
VPD  N23   N3   N   0  1  N  N  N  35.784  -31.191  -36.424   5.335  -1.667   0.082  N23   VPD  27  
VPD  C25   C17  C   0  1  N  N  N  34.517  -32.776  -37.956   7.241  -3.092   0.712  C25   VPD  28  
VPD  C26   C18  C   0  1  N  N  N  33.435  -31.775  -38.450   8.292  -3.484  -0.347  C26   VPD  29  
VPD  C28   C19  C   0  1  N  N  N  35.662  -30.907  -38.799   7.557  -1.244  -0.899  C28   VPD  30  
VPD  N29   N4   N   0  1  Y  N  N  36.780  -30.646  -34.421   5.187   0.617   0.639  N29   VPD  31  
VPD  CL31  CL1  CL  0  0  N  N  N  37.500  -30.073  -31.938   5.321   3.164   1.318  CL31  VPD  32  
VPD  N32   N5   N   0  1  Y  N  N  39.040  -30.298  -34.065   3.199   1.801   0.555  N32   VPD  33  
VPD  O36   O8   O   0  1  N  N  N  42.968  -31.635  -33.865   0.559   2.973  -2.004  O36   VPD  34  
VPD  O39   O9   O   0  1  N  N  N  44.457  -32.657  -35.874  -1.792   3.768  -1.227  O39   VPD  35  
VPD  H1    H1   H   0  1  N  N  N  47.385  -27.546  -37.826  -6.356  -1.752   1.980  H1    VPD  36  
VPD  H2    H2   H   0  1  N  N  N  47.342  -27.121  -39.570  -4.658  -1.683   2.510  H2    VPD  37  
VPD  H3    H3   H   0  1  N  N  N  46.264  -30.680  -39.593  -6.295   1.238   0.868  H3    VPD  38  
VPD  H4    H4   H   0  1  N  N  N  47.318  -29.469  -40.400  -5.950   0.706  -0.795  H4    VPD  39  
VPD  H5    H5   H   0  1  N  N  N  44.079  -30.568  -38.465  -3.108  -0.043  -1.031  H5    VPD  40  
VPD  H6    H6   H   0  1  N  N  N  45.545  -30.964  -37.505  -4.180   1.363  -0.820  H6    VPD  41  
VPD  H7    H7   H   0  1  N  N  N  41.647  -29.682  -34.563   0.405   2.313   0.476  H7    VPD  42  
VPD  H8    H8   H   0  1  N  N  N  36.683  -32.542  -37.814   6.995  -0.990   1.185  H8    VPD  43  
VPD  H9    H9   H   0  1  N  N  N  34.049  -29.746  -37.878   9.570  -1.717  -0.185  H9    VPD  44  
VPD  H10   H10  H   0  1  N  N  N  33.865  -29.986  -39.648   9.249  -2.239  -1.870  H10   VPD  45  
VPD  H11   H11  H   0  1  N  N  N  41.572  -32.440  -35.221  -0.202   1.051  -2.256  H11   VPD  46  
VPD  H12   H12  H   0  1  N  N  N  42.901  -32.135  -37.191  -2.340   2.025  -2.216  H12   VPD  47  
VPD  H13   H13  H   0  1  N  N  N  44.194  -29.845  -41.666  -6.912  -2.535  -0.571  H13   VPD  48  
VPD  H14   H14  H   0  1  N  N  N  43.684  -26.473  -40.407  -4.566  -1.993  -2.612  H14   VPD  49  
VPD  H15   H15  H   0  1  N  N  N  46.397  -25.489  -38.225  -6.071  -0.319   3.870  H15   VPD  50  
VPD  H16   H16  H   0  1  N  N  N  49.554  -31.218  -38.165  -8.687   1.282   0.359  H16   VPD  51  
VPD  H17   H17  H   0  1  N  N  N  48.223  -31.990  -39.092  -8.343   0.750  -1.304  H17   VPD  52  
VPD  H18   H18  H   0  1  N  N  N  49.262  -30.752  -39.875  -9.438  -0.202  -0.274  H18   VPD  53  
VPD  H19   H19  H   0  1  N  N  N  44.437  -30.092  -35.461  -2.429   2.396   0.678  H19   VPD  54  
VPD  H20   H20  H   0  1  N  N  N  38.396  -31.233  -38.456   2.486  -2.482  -0.673  H20   VPD  55  
VPD  H21   H21  H   0  1  N  N  N  35.337  -30.317  -36.615   4.898  -2.481  -0.212  H21   VPD  56  
VPD  H22   H22  H   0  1  N  N  N  34.188  -33.271  -37.031   7.690  -3.104   1.705  H22   VPD  57  
VPD  H23   H23  H   0  1  N  N  N  34.718  -33.535  -38.726   6.398  -3.782   0.675  H23   VPD  58  
VPD  H24   H24  H   0  1  N  N  N  32.662  -31.632  -37.681   7.826  -4.048  -1.156  H24   VPD  59  
VPD  H25   H25  H   0  1  N  N  N  32.968  -32.139  -39.377   9.096  -4.063   0.108  H25   VPD  60  
VPD  H26   H26  H   0  1  N  N  N  35.876  -31.358  -39.779   6.972  -1.446  -1.796  H26   VPD  61  
VPD  H27   H27  H   0  1  N  N  N  36.347  -30.064  -38.627   7.825  -0.189  -0.845  H27   VPD  62  
VPD  H28   H28  H   0  1  N  N  N  42.305  -31.538  -33.191   0.354   3.283  -2.897  H28   VPD  63  
VPD  H29   H29  H   0  1  N  N  N  44.154  -33.555  -35.816  -1.465   4.259  -1.993  H29   VPD  64  
#   #
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
VPD  O1   P2    DOUB  N  N   1  
VPD  O3   P2    SING  N  N   2  
VPD  P2   O4    SING  N  N   3  
VPD  P2   C5    SING  N  N   4  
VPD  C8   C5    SING  N  N   5  
VPD  C8   O9    SING  N  N   6  
VPD  C5   C6    SING  N  N   7  
VPD  C5   O11   SING  N  N   8  
VPD  C10  O9    SING  N  N   9  
VPD  C28  C27   SING  N  N  10  
VPD  C28  C24   SING  N  N  11  
VPD  C27  C26   SING  N  N  12  
VPD  C6   O7    SING  N  N  13  
VPD  C26  C25   SING  N  N  14  
VPD  C25  C24   SING  N  N  15  
VPD  O11  C12   SING  N  N  16  
VPD  C24  N23   SING  N  N  17  
VPD  C12  C13   SING  N  N  18  
VPD  C20  N19   DOUB  Y  N  19  
VPD  C20  C21   SING  Y  N  20  
VPD  N19  N18   SING  Y  N  21  
VPD  O15  C13   SING  N  N  22  
VPD  O15  C16   SING  N  N  23  
VPD  N23  C22   SING  N  N  24  
VPD  C13  C37   SING  N  N  25  
VPD  C21  C22   DOUB  Y  N  26  
VPD  C21  C33   SING  Y  N  27  
VPD  C37  O39   SING  N  N  28  
VPD  C37  C34   SING  N  N  29  
VPD  N18  C16   SING  N  N  30  
VPD  N18  C33   SING  Y  N  31  
VPD  C22  N29   SING  Y  N  32  
VPD  C16  C34   SING  N  N  33  
VPD  C33  N32   DOUB  Y  N  34  
VPD  C34  O36   SING  N  N  35  
VPD  N29  C30   DOUB  Y  N  36  
VPD  N32  C30   SING  Y  N  37  
VPD  C30  CL31  SING  N  N  38  
VPD  C6   H1    SING  N  N  39  
VPD  C6   H2    SING  N  N  40  
VPD  C8   H3    SING  N  N  41  
VPD  C8   H4    SING  N  N  42  
VPD  C12  H5    SING  N  N  43  
VPD  C12  H6    SING  N  N  44  
VPD  C16  H7    SING  N  N  45  
VPD  C24  H8    SING  N  N  46  
VPD  C27  H9    SING  N  N  47  
VPD  C27  H10   SING  N  N  48  
VPD  C34  H11   SING  N  N  49  
VPD  C37  H12   SING  N  N  50  
VPD  O3   H13   SING  N  N  51  
VPD  O4   H14   SING  N  N  52  
VPD  O7   H15   SING  N  N  53  
VPD  C10  H16   SING  N  N  54  
VPD  C10  H17   SING  N  N  55  
VPD  C10  H18   SING  N  N  56  
VPD  C13  H19   SING  N  N  57  
VPD  C20  H20   SING  N  N  58  
VPD  N23  H21   SING  N  N  59  
VPD  C25  H22   SING  N  N  60  
VPD  C25  H23   SING  N  N  61  
VPD  C26  H24   SING  N  N  62  
VPD  C26  H25   SING  N  N  63  
VPD  C28  H26   SING  N  N  64  
VPD  C28  H27   SING  N  N  65  
VPD  O36  H28   SING  N  N  66  
VPD  O39  H29   SING  N  N  67  
#   #
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
VPD  SMILES            ACDLabs               12.01  "C(CO)(OCC1C(C(C(O1)n4c2c(c(nc(Cl)n2)NC3CCCC3)cn4)O)O)(COC)P(=O)(O)O"  
VPD  InChI             InChI                 1.03   "InChI=1S/C19H29ClN5O9P/c1-32-9-19(8-26,35(29,30)31)33-7-12-13(27)14(28)17(34-12)25-16-11(6-21-25)15(23-18(20)24-16)22-10-4-2-3-5-10/h6,10,12-14,17,26-28H,2-5,7-9H2,1H3,(H,22,23,24)(H2,29,30,31)/t12-,13-,14-,17-,19-/m1/s1"  
VPD  InChIKey          InChI                 1.03   BQCRMLSBGAKPFW-RTPDKIPNSA-N  
VPD  SMILES_CANONICAL  CACTVS                3.385  "COC[C@](CO)(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2ncc3c(NC4CCCC4)nc(Cl)nc23)[P](O)(O)=O"  
VPD  SMILES            CACTVS                3.385  "COC[C](CO)(OC[CH]1O[CH]([CH](O)[CH]1O)n2ncc3c(NC4CCCC4)nc(Cl)nc23)[P](O)(O)=O"  
VPD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "COC[C@](CO)(OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(cn2)c(nc(n3)Cl)NC4CCCC4)O)O)P(=O)(O)O"  
VPD  SMILES            "OpenEye OEToolkits"  2.0.7  "COCC(CO)(OCC1C(C(C(O1)n2c3c(cn2)c(nc(n3)Cl)NC4CCCC4)O)O)P(=O)(O)O"  
#   #
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
VPD  "SYSTEMATIC NAME"  ACDLabs               12.01  "6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine"  
VPD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-(cyclopentylamino)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]-1-methoxy-3-oxidanyl-propan-2-yl]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
VPD  "Create component"  2020-08-31  RCSB  
VPD  "Initial release"   2020-09-23  RCSB  
VPD  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VPD
_pdbx_chem_comp_synonyms.name        OP-0105244
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
