data_OH9 # _chem_comp.id OH9 _chem_comp.name "beta-methyl-adenosine diphosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N5 O10 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] methyl hydrogen phosphate; [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] methyl hydrogen phosphate; beta-methyl-ADP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-09-07 _chem_comp.pdbx_modified_date 2024-03-15 _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 441.228 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OH9 _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 8AZP _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 OH9 C2 C1 C 0 1 Y N N N N N 21.265 -0.756 -7.791 6.739 -0.416 1.198 C2 OH9 1 OH9 C4 C2 C 0 1 Y N N N N N 22.100 -2.808 -7.059 4.601 -0.529 0.362 C4 OH9 2 OH9 C01 C3 C 0 1 N N N N N N 18.490 -10.747 -1.990 -7.058 -2.789 1.441 C01 OH9 3 OH9 "C5'" C4 C 0 1 N N N N N N 19.724 -7.539 -7.078 -0.825 1.754 -0.548 "C5'" OH9 4 OH9 "C4'" C5 C 0 1 N N R N N N 20.348 -6.863 -8.221 0.395 1.834 0.373 "C4'" OH9 5 OH9 "C1'" C6 C 0 1 N N R N N N 21.914 -5.044 -8.021 2.486 0.851 0.528 "C1'" OH9 6 OH9 C8 C7 C 0 1 Y N N N N N 23.080 -4.365 -5.880 2.861 -1.287 -0.760 C8 OH9 7 OH9 C5 C8 C 0 1 Y N N N N N 22.639 -2.234 -5.940 4.938 -1.717 -0.308 C5 OH9 8 OH9 C6 C9 C 0 1 Y N N N N N 22.470 -0.815 -5.799 6.249 -2.206 -0.174 C6 OH9 9 OH9 "C2'" C10 C 0 1 N N R N N N 22.633 -6.452 -7.929 2.697 2.084 -0.387 "C2'" OH9 10 OH9 "C3'" C11 C 0 1 N N S N N N 21.554 -7.350 -8.624 1.389 2.881 -0.163 "C3'" OH9 11 OH9 N9 N1 N 0 1 Y N N N N N 22.385 -4.116 -7.007 3.286 -0.283 0.059 N9 OH9 12 OH9 N7 N2 N 0 1 Y N N N N N 23.262 -3.230 -5.231 3.832 -2.127 -0.974 N7 OH9 13 OH9 N6 N3 N 0 1 N N N N N N 23.004 -0.119 -4.671 6.639 -3.371 -0.811 N6 OH9 14 OH9 N1 N4 N 0 1 Y N N N N N 21.789 -0.149 -6.705 7.102 -1.529 0.587 N1 OH9 15 OH9 N3 N5 N 0 1 Y N N N N N 21.401 -2.075 -7.967 5.525 0.082 1.098 N3 OH9 16 OH9 O1B O1 O 0 1 N N N N N N 19.159 -11.223 -3.144 -5.810 -2.111 1.276 O1B OH9 17 OH9 O2B O2 O 0 1 N N N N N N 17.186 -10.551 -4.742 -6.501 0.392 0.867 O2B OH9 18 OH9 O3B O3 O 0 1 N N N N N N 19.471 -11.255 -5.728 -6.078 -1.186 -1.057 O3B OH9 19 OH9 O3A O4 O 0 1 N N N N N N 19.106 -8.961 -4.508 -4.072 -0.416 0.268 O3A OH9 20 OH9 O1A O5 O 0 1 N N N N N N 21.682 -9.140 -4.165 -3.924 1.791 -0.947 O1A OH9 21 OH9 O2A O6 O 0 1 N N N N N N 20.467 -6.967 -3.841 -2.932 -0.227 -2.094 O2A OH9 22 OH9 "O5'" O7 O 0 1 N N N N N N 20.820 -7.980 -6.200 -1.785 0.854 0.010 "O5'" OH9 23 OH9 "O4'" O8 O 0 1 N N N N N N 20.637 -5.291 -7.751 1.076 0.568 0.393 "O4'" OH9 24 OH9 "O2'" O9 O 0 1 N N N N N N 23.852 -6.438 -8.546 3.835 2.840 0.031 "O2'" OH9 25 OH9 "O3'" O10 O 0 1 N N N N N N 21.665 -7.230 -10.094 1.594 3.917 0.800 "O3'" OH9 26 OH9 PB P1 P 0 1 N N N N N N 18.709 -10.552 -4.591 -5.625 -0.838 0.309 PB OH9 27 OH9 PA P2 P 0 1 N N N N N N 20.573 -8.274 -4.620 -3.194 0.528 -0.696 PA OH9 28 OH9 H2 H1 H 0 1 N N N N N N 20.731 -0.171 -8.525 7.465 0.103 1.808 H2 OH9 29 OH9 H1 H2 H 0 1 N N N N N N 18.876 -11.267 -1.101 -7.801 -2.092 1.828 H1 OH9 30 OH9 H3 H3 H 0 1 N N N N N N 18.663 -9.666 -1.886 -7.390 -3.177 0.479 H3 OH9 31 OH9 H4 H4 H 0 1 N N N N N N 17.411 -10.938 -2.087 -6.933 -3.614 2.143 H4 OH9 32 OH9 "H5'1" H5 H 0 0 N N N N N N 19.063 -6.843 -6.540 -1.270 2.744 -0.648 "H5'1" OH9 33 OH9 "H5'2" H6 H 0 0 N N N N N N 19.141 -8.406 -7.422 -0.516 1.393 -1.529 "H5'2" OH9 34 OH9 "H4'" H7 H 0 1 N N N N N N 19.636 -6.825 -9.059 0.080 2.101 1.382 "H4'" OH9 35 OH9 "H1'" H8 H 0 1 N N N N N N 22.065 -4.630 -9.029 2.731 1.094 1.562 "H1'" OH9 36 OH9 H8 H9 H 0 1 N N N N N N 23.431 -5.335 -5.560 1.866 -1.372 -1.170 H8 OH9 37 OH9 "H2'" H10 H 0 1 N N N N N N 22.712 -6.741 -6.871 2.795 1.782 -1.430 "H2'" OH9 38 OH9 "H3'" H11 H 0 1 N N N N N N 21.702 -8.395 -8.315 1.032 3.300 -1.104 "H3'" OH9 39 OH9 HN61 H12 H 0 0 N N N N N N 22.767 0.850 -4.734 6.004 -3.860 -1.358 HN61 OH9 40 OH9 HN62 H13 H 0 0 N N N N N N 22.620 -0.502 -3.831 7.546 -3.698 -0.711 HN62 OH9 41 OH9 HOB2 H14 H 0 0 N N N N N N 16.946 -11.001 -5.543 -6.258 0.674 1.760 HOB2 OH9 42 OH9 HOA2 H15 H 0 0 N N N N N N 21.150 -6.935 -3.181 -2.457 -1.065 -2.005 HOA2 OH9 43 OH9 "HO2'" H16 H 0 0 N N N N N N 24.445 -5.873 -8.064 4.008 3.622 -0.511 "HO2'" OH9 44 OH9 "HO3'" H17 H 0 0 N N N N N N 22.506 -7.569 -10.377 2.211 4.604 0.515 "HO3'" OH9 45 # 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 OH9 "O3'" "C3'" SING N N 1 OH9 "C3'" "C4'" SING N N 2 OH9 "C3'" "C2'" SING N N 3 OH9 "O2'" "C2'" SING N N 4 OH9 "C4'" "O4'" SING N N 5 OH9 "C4'" "C5'" SING N N 6 OH9 "C1'" "C2'" SING N N 7 OH9 "C1'" "O4'" SING N N 8 OH9 "C1'" N9 SING N N 9 OH9 N3 C2 DOUB Y N 10 OH9 N3 C4 SING Y N 11 OH9 C2 N1 SING Y N 12 OH9 "C5'" "O5'" SING N N 13 OH9 C4 N9 SING Y N 14 OH9 C4 C5 DOUB Y N 15 OH9 N9 C8 SING Y N 16 OH9 N1 C6 DOUB Y N 17 OH9 "O5'" PA SING N N 18 OH9 C5 C6 SING Y N 19 OH9 C5 N7 SING Y N 20 OH9 C8 N7 DOUB Y N 21 OH9 C6 N6 SING N N 22 OH9 O3B PB DOUB N N 23 OH9 O2B PB SING N N 24 OH9 PA O3A SING N N 25 OH9 PA O1A DOUB N N 26 OH9 PA O2A SING N N 27 OH9 PB O3A SING N N 28 OH9 PB O1B SING N N 29 OH9 O1B C01 SING N N 30 OH9 C2 H2 SING N N 31 OH9 C01 H1 SING N N 32 OH9 C01 H3 SING N N 33 OH9 C01 H4 SING N N 34 OH9 "C5'" "H5'1" SING N N 35 OH9 "C5'" "H5'2" SING N N 36 OH9 "C4'" "H4'" SING N N 37 OH9 "C1'" "H1'" SING N N 38 OH9 C8 H8 SING N N 39 OH9 "C2'" "H2'" SING N N 40 OH9 "C3'" "H3'" SING N N 41 OH9 N6 HN61 SING N N 42 OH9 N6 HN62 SING N N 43 OH9 O2B HOB2 SING N N 44 OH9 O2A HOA2 SING N N 45 OH9 "O2'" "HO2'" SING N N 46 OH9 "O3'" "HO3'" SING N N 47 # 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 OH9 InChI InChI 1.06 "InChI=1S/C11H17N5O10P2/c1-23-27(19,20)26-28(21,22)24-2-5-7(17)8(18)11(25-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H,21,22)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1" OH9 InChIKey InChI 1.06 RUEXVBUEYZJEHS-IOSLPCCCSA-N OH9 SMILES_CANONICAL CACTVS 3.385 "CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" OH9 SMILES CACTVS 3.385 "CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" OH9 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" OH9 SMILES "OpenEye OEToolkits" 3.1.0.0 "COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" # _pdbx_chem_comp_identifier.comp_id OH9 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _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] 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 OH9 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] methyl hydrogen phosphate" PDB ? 2 OH9 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] methyl hydrogen phosphate" PUBCHEM ? 3 OH9 beta-methyl-ADP 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 OH9 "Create component" 2022-09-08 PDBE OH9 "Initial release" 2024-03-20 RCSB #