data_RVK
#

_chem_comp.id                                   RVK
_chem_comp.name                                 "Adenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl] estere"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H25 N5 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; [[(2R,3S,4R,5R)-5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5S)-3,4-dihydroxy-5-methoxyoxolan-2-yl]methyl hydrogen phosphate; J3.653.949F; alpha-1''-O-methyl-ADP ribose"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-10-23
_chem_comp.pdbx_modified_date                   2021-06-11
_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                       573.342
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    RVK
_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       7AQM
_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
RVK  C1     C1   C  0  1  N  N  N   7.627   0.534  12.440  -5.351   2.935  -3.362  C1     RVK   1  
RVK  C2     C2   C  0  1  Y  N  N  15.695  -8.672   3.893   7.192   3.214  -1.145  C2     RVK   2  
RVK  C4     C3   C  0  1  Y  N  N  15.589  -6.744   4.925   5.738   1.786  -0.082  C4     RVK   3  
RVK  C5     C4   C  0  1  Y  N  N  16.910  -6.460   4.689   5.928   2.500   1.114  C5     RVK   4  
RVK  C6     C5   C  0  1  Y  N  N  17.628  -7.405   3.985   6.791   3.608   1.094  C6     RVK   5  
RVK  "C1'"  C6   C  0  1  N  N  R  13.788  -5.384   6.177   4.348  -0.232  -0.715  "C1'"  RVK   6  
RVK  C1D    C7   C  0  1  N  N  S  10.011   0.489  11.903  -6.767   2.189  -1.579  C1D    RVK   7  
RVK  "C2'"  C8   C  0  1  N  N  R  13.296  -6.449   7.157   5.293  -1.454  -0.747  "C2'"  RVK   8  
RVK  C2D    C9   C  0  1  N  N  R  10.928   1.593  12.404  -7.527   2.692  -0.336  C2D    RVK   9  
RVK  "C3'"  C10  C  0  1  N  N  S  13.537  -5.824   8.512   4.339  -2.662  -0.883  "C3'"  RVK  10  
RVK  C3D    C11  C  0  1  N  N  S  11.446   2.194  11.073  -7.035   1.773   0.808  C3D    RVK  11  
RVK  "C4'"  C12  C  0  1  N  N  R  13.210  -4.375   8.159   2.931  -2.028  -0.917  "C4'"  RVK  12  
RVK  C4D    C13  C  0  1  N  N  R  11.518   0.970  10.170  -5.696   1.237   0.240  C4D    RVK  13  
RVK  "C5'"  C14  C  0  1  N  N  N  13.671  -3.287   9.082   1.932  -2.907  -0.162  "C5'"  RVK  14  
RVK  C5D    C15  C  0  1  N  N  N  12.905   0.470   9.903  -5.334  -0.103   0.886  C5D    RVK  15  
RVK  C8     C16  C  0  1  Y  N  N  16.187  -4.817   5.762   4.534   0.893   1.535  C8     RVK  16  
RVK  N1     N1   N  0  1  Y  N  N  16.976  -8.527   3.594   7.398   3.918  -0.047  N1     RVK  17  
RVK  N3     N2   N  0  1  Y  N  N  14.923  -7.841   4.554   6.384   2.175  -1.176  N3     RVK  18  
RVK  N6     N3   N  0  1  N  N  N  18.913  -7.232   3.692   7.017   4.350   2.241  N6     RVK  19  
RVK  N7     N4   N  0  1  Y  N  N  17.286  -5.244   5.209   5.165   1.903   2.061  N7     RVK  20  
RVK  N9     N5   N  0  1  Y  N  N  15.117  -5.668   5.633   4.854   0.780   0.215  N9     RVK  21  
RVK  O1A    O1   O  0  1  N  N  N  14.601  -4.471  11.489  -0.943  -4.480  -0.299  O1A    RVK  22  
RVK  O1B    O2   O  0  1  N  N  N  15.619  -0.043  12.575  -4.341  -3.185   0.366  O1B    RVK  23  
RVK  O1D    O3   O  0  1  N  N  N   8.673   0.979  11.550  -5.924   3.225  -2.086  O1D    RVK  24  
RVK  "O2'"  O4   O  0  1  N  N  N  11.944  -6.737   6.940   6.170  -1.380  -1.873  "O2'"  RVK  25  
RVK  O2A    O5   O  0  1  N  N  N  16.808  -3.171  10.977  -0.468  -3.192   1.819  O2A    RVK  26  
RVK  O2B    O6   O  0  1  N  N  N  15.736  -0.388   9.956  -3.244  -1.960   2.281  O2B    RVK  27  
RVK  O2D    O7   O  0  1  N  N  N  10.420   2.382  13.469  -7.193   4.054  -0.063  O2D    RVK  28  
RVK  "O3'"  O8   O  0  1  N  N  N  12.709  -6.404   9.507   4.598  -3.371  -2.096  "O3'"  RVK  29  
RVK  O3A    O9   O  0  1  N  N  N  14.773  -1.998  11.569  -1.964  -2.092   0.109  O3A    RVK  30  
RVK  O3D    O10  O  0  1  N  N  N  10.796   3.267  10.362  -6.818   2.521   2.006  O3D    RVK  31  
RVK  "O4'"  O11  O  0  1  N  N  N  13.846  -4.176   6.887   3.084  -0.755  -0.251  "O4'"  RVK  32  
RVK  O4D    O12  O  0  1  N  N  N  10.913  -0.070  10.913  -5.972   1.065  -1.167  O4D    RVK  33  
RVK  "O5'"  O13  O  0  1  N  N  N  15.064  -3.398   9.348   0.618  -2.364  -0.303  "O5'"  RVK  34  
RVK  O5D    O14  O  0  1  N  N  N  13.709   0.309  11.136  -4.092  -0.568   0.354  O5D    RVK  35  
RVK  PA     P1   P  0  1  N  N  N  15.334  -3.333  10.897  -0.684  -3.036   0.364  PA     RVK  36  
RVK  PB     P2   P  0  1  N  N  N  15.107  -0.478  11.279  -3.407  -1.952   0.810  PB     RVK  37  
RVK  H1     H1   H  0  1  N  N  N   6.662   0.944  12.106  -4.744   2.033  -3.291  H1     RVK  38  
RVK  H2     H2   H  0  1  N  N  N   7.581  -0.565  12.431  -6.146   2.782  -4.091  H2     RVK  39  
RVK  H3     H3   H  0  1  N  N  N   7.841   0.884  13.461  -4.725   3.770  -3.677  H3     RVK  40  
RVK  H4     H4   H  0  1  N  N  N  15.228  -9.584   3.552   7.701   3.504  -2.051  H4     RVK  41  
RVK  H5     H5   H  0  1  N  N  N  13.065  -5.307   5.352   4.240   0.190  -1.714  H5     RVK  42  
RVK  H6     H6   H  0  1  N  N  N   9.901  -0.241  12.718  -7.477   1.879  -2.347  H6     RVK  43  
RVK  H7     H7   H  0  1  N  N  N  13.916  -7.352   7.053   5.863  -1.520   0.179  H7     RVK  44  
RVK  H8     H8   H  0  1  N  N  N  11.798   1.062  12.818  -8.603   2.585  -0.478  H8     RVK  45  
RVK  H9     H9   H  0  1  N  N  N  14.601  -5.909   8.779   4.440  -3.327  -0.024  H9     RVK  46  
RVK  H10    H10  H  0  1  N  N  N  12.484   2.505  11.261  -7.737   0.958   0.982  H10    RVK  47  
RVK  H11    H11  H  0  1  N  N  N  12.120  -4.290   8.038   2.605  -1.883  -1.947  H11    RVK  48  
RVK  H12    H12  H  0  1  N  N  N  10.987   1.162   9.226  -4.897   1.963   0.389  H12    RVK  49  
RVK  H13    H13  H  0  1  N  N  N  13.471  -2.311   8.615   1.955  -3.917  -0.572  H13    RVK  50  
RVK  H14    H14  H  0  1  N  N  N  13.117  -3.361  10.030   2.201  -2.938   0.894  H14    RVK  51  
RVK  H15    H15  H  0  1  N  N  N  12.835  -0.506   9.400  -5.243   0.027   1.964  H15    RVK  52  
RVK  H16    H16  H  0  1  N  N  N  13.415   1.187   9.243  -6.117  -0.831   0.673  H16    RVK  53  
RVK  H17    H17  H  0  1  N  N  N  16.122  -3.871   6.280   3.856   0.242   2.067  H17    RVK  54  
RVK  H18    H18  H  0  1  N  N  N  19.248  -8.023   3.180   6.578   4.106   3.070  H18    RVK  55  
RVK  H19    H19  H  0  1  N  N  N  19.020  -6.406   3.138   7.616   5.113   2.215  H19    RVK  56  
RVK  H20    H20  H  0  1  N  N  N  15.216  -5.058  11.913  -1.092  -4.454  -1.254  H20    RVK  57  
RVK  H21    H21  H  0  1  N  N  N  16.481   0.340  12.463  -4.492  -3.242  -0.587  H21    RVK  58  
RVK  H22    H22  H  0  1  N  N  N  11.658  -7.400   7.558   6.785  -2.122  -1.942  H22    RVK  59  
RVK  H23    H23  H  0  1  N  N  N  10.159   1.816  14.186  -7.426   4.667  -0.774  H23    RVK  60  
RVK  H24    H24  H  0  1  N  N  N  12.883  -5.991  10.345   5.491  -3.740  -2.154  H24    RVK  61  
RVK  H25    H25  H  0  1  N  N  N  10.748   4.034  10.920  -7.612   2.952   2.350  H25    RVK  62  
#   #
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
RVK  N1     C2     DOUB  Y  N   1  
RVK  N1     C6     SING  Y  N   2  
RVK  N6     C6     SING  N  N   3  
RVK  C2     N3     SING  Y  N   4  
RVK  C6     C5     DOUB  Y  N   5  
RVK  N3     C4     DOUB  Y  N   6  
RVK  C5     C4     SING  Y  N   7  
RVK  C5     N7     SING  Y  N   8  
RVK  C4     N9     SING  Y  N   9  
RVK  N7     C8     DOUB  Y  N  10  
RVK  N9     C8     SING  Y  N  11  
RVK  N9     "C1'"  SING  N  N  12  
RVK  "C1'"  "O4'"  SING  N  N  13  
RVK  "C1'"  "C2'"  SING  N  N  14  
RVK  "O4'"  "C4'"  SING  N  N  15  
RVK  "O2'"  "C2'"  SING  N  N  16  
RVK  "C2'"  "C3'"  SING  N  N  17  
RVK  "C4'"  "C3'"  SING  N  N  18  
RVK  "C4'"  "C5'"  SING  N  N  19  
RVK  "C3'"  "O3'"  SING  N  N  20  
RVK  "C5'"  "O5'"  SING  N  N  21  
RVK  "O5'"  PA     SING  N  N  22  
RVK  C5D    C4D    SING  N  N  23  
RVK  C5D    O5D    SING  N  N  24  
RVK  O2B    PB     DOUB  N  N  25  
RVK  C4D    O4D    SING  N  N  26  
RVK  C4D    C3D    SING  N  N  27  
RVK  O3D    C3D    SING  N  N  28  
RVK  PA     O2A    DOUB  N  N  29  
RVK  PA     O1A    SING  N  N  30  
RVK  PA     O3A    SING  N  N  31  
RVK  O4D    C1D    SING  N  N  32  
RVK  C3D    C2D    SING  N  N  33  
RVK  O5D    PB     SING  N  N  34  
RVK  PB     O3A    SING  N  N  35  
RVK  PB     O1B    SING  N  N  36  
RVK  O1D    C1D    SING  N  N  37  
RVK  O1D    C1     SING  N  N  38  
RVK  C1D    C2D    SING  N  N  39  
RVK  C2D    O2D    SING  N  N  40  
RVK  C1     H1     SING  N  N  41  
RVK  C1     H2     SING  N  N  42  
RVK  C1     H3     SING  N  N  43  
RVK  C2     H4     SING  N  N  44  
RVK  "C1'"  H5     SING  N  N  45  
RVK  C1D    H6     SING  N  N  46  
RVK  "C2'"  H7     SING  N  N  47  
RVK  C2D    H8     SING  N  N  48  
RVK  "C3'"  H9     SING  N  N  49  
RVK  C3D    H10    SING  N  N  50  
RVK  "C4'"  H11    SING  N  N  51  
RVK  C4D    H12    SING  N  N  52  
RVK  "C5'"  H13    SING  N  N  53  
RVK  "C5'"  H14    SING  N  N  54  
RVK  C5D    H15    SING  N  N  55  
RVK  C5D    H16    SING  N  N  56  
RVK  C8     H17    SING  N  N  57  
RVK  N6     H18    SING  N  N  58  
RVK  N6     H19    SING  N  N  59  
RVK  O1A    H20    SING  N  N  60  
RVK  O1B    H21    SING  N  N  61  
RVK  "O2'"  H22    SING  N  N  62  
RVK  O2D    H23    SING  N  N  63  
RVK  "O3'"  H24    SING  N  N  64  
RVK  O3D    H25    SING  N  N  65  
#   #
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
RVK  InChI             InChI                 1.03   "InChI=1S/C16H25N5O14P2/c1-30-16-12(25)10(23)7(34-16)3-32-37(28,29)35-36(26,27)31-2-6-9(22)11(24)15(33-6)21-5-20-8-13(17)18-4-19-14(8)21/h4-7,9-12,15-16,22-25H,2-3H2,1H3,(H,26,27)(H,28,29)(H2,17,18,19)/t6-,7-,9-,10-,11-,12-,15-,16+/m1/s1"  
RVK  InChIKey          InChI                 1.03   XNNSDOSOBTWHPT-DBXCYWGHSA-N  
RVK  SMILES_CANONICAL  CACTVS                3.385  "CO[C@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O"  
RVK  SMILES            CACTVS                3.385  "CO[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O"  
RVK  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CO[C@@H]1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O"  
RVK  SMILES            "OpenEye OEToolkits"  2.0.7  "COC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          RVK
_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~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
#   #
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  RVK  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"  PDB      ?  
2  RVK  "[[(2R,3S,4R,5R)-5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5S)-3,4-dihydroxy-5-methoxyoxolan-2-yl]methyl hydrogen phosphate"                                    PUBCHEM  ?  
3  RVK  "Adenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl] ester"                                                                                         PUBCHEM  ?  
4  RVK  "alpha-1''-O-methyl-ADP ribose"                                                                                                                                                                            AUTHOR   ?  
5  RVK  J3.653.949F                                                                                                                                                                                                AUTHOR   ?  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RVK  "Create component"  2020-10-23  PDBE  
RVK  "Modify synonyms"   2021-03-08  PDBE  
RVK  "Initial release"   2021-06-16  RCSB  
##
