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 
# 
