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 ##