data_8NK
# 
_chem_comp.id                                    8NK 
_chem_comp.name                                  
;7-methylguanosine 5'-diphosphate
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H18 N5 O11 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2017-02-13 
_chem_comp.pdbx_modified_date                    2024-02-25 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_chem_comp.pdbx_replaced_by                      M7G 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        458.235 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8NK 
_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        5N2V 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
8NK PA    P1  P 0 1 N N N N N N 17.775 11.796 2.094  3.846  0.247  0.582  PA    8NK 1  
8NK O1A   O1  O 0 1 N N N N N N 17.587 10.378 2.468  4.649  1.419  0.997  O1A   8NK 2  
8NK O2A   O2  O 0 1 N N N N N N 18.805 12.450 3.006  3.592  -0.706 1.855  O2A   8NK 3  
8NK O3A   O3  O 0 1 N N N N N N 16.404 12.588 2.249  4.641  -0.574 -0.552 O3A   8NK 4  
8NK "O5'" O4  O 0 1 N N N N N N 18.182 12.036 0.589  2.433  0.746  -0.006 "O5'" 8NK 5  
8NK PB    P2  P 0 1 N N N N N N 15.419 12.829 3.477  6.167  -1.056 -0.722 PB    8NK 6  
8NK O1B   O5  O 0 1 N N N N N N 14.096 12.221 3.171  6.647  -1.635 0.553  O1B   8NK 7  
8NK O2B   O6  O 0 1 N N N N N N 15.351 14.346 3.683  6.253  -2.168 -1.883 O2B   8NK 8  
8NK O3B   O7  O 0 1 N N N N N N 16.091 12.207 4.701  7.087  0.205  -1.118 O3B   8NK 9  
8NK "C5'" C1  C 0 1 N N N N N N 17.369 12.521 -0.501 1.541  1.590  0.724  "C5'" 8NK 10 
8NK "C4'" C2  C 0 1 N N R N N N 18.295 12.887 -1.632 0.297  1.870  -0.122 "C4'" 8NK 11 
8NK "O4'" O8  O 0 1 N N N N N N 19.332 13.736 -1.114 -0.450 0.657  -0.310 "O4'" 8NK 12 
8NK "C3'" C3  C 0 1 N N S N N N 18.992 11.693 -2.279 -0.623 2.866  0.611  "C3'" 8NK 13 
8NK "O3'" O9  O 0 1 N N N N N N 18.354 11.353 -3.505 -0.802 4.049  -0.169 "O3'" 8NK 14 
8NK "C2'" C4  C 0 1 N N R N N N 20.444 12.159 -2.504 -1.962 2.104  0.762  "C2'" 8NK 15 
8NK "O2'" O10 O 0 1 N N N N N N 20.760 12.257 -3.888 -3.071 2.970  0.513  "O2'" 8NK 16 
8NK "C1'" C5  C 0 1 N N R N N N 20.526 13.536 -1.833 -1.847 1.022  -0.342 "C1'" 8NK 17 
8NK N9    N1  N 0 1 Y N N N N N 21.640 13.651 -0.881 -2.689 -0.133 -0.022 N9    8NK 18 
8NK C8    C6  C 0 1 Y N N N N N 21.471 13.857 0.426  -2.289 -1.273 0.613  C8    8NK 19 
8NK N7    N2  N 1 1 Y N N N N N 22.656 13.924 1.007  -3.296 -2.088 0.733  N7    8NK 20 
8NK CM7   C7  C 0 1 N N N N N N 22.872 14.148 2.441  -3.247 -3.409 1.362  CM7   8NK 21 
8NK C5    C8  C 0 1 Y N N N N N 23.636 13.752 0.039  -4.399 -1.522 0.183  C5    8NK 22 
8NK C6    C9  C 0 1 N N N N N N 25.055 13.729 0.092  -5.743 -1.933 0.027  C6    8NK 23 
8NK O6    O11 O 0 1 N N N N N N 25.785 13.866 1.070  -6.116 -3.019 0.438  O6    8NK 24 
8NK N1    N3  N 0 1 N N N N N N 25.584 13.514 -1.169 -6.604 -1.092 -0.587 N1    8NK 25 
8NK C2    C10 C 0 1 N N N N N N 24.861 13.342 -2.321 -6.177 0.120  -1.041 C2    8NK 26 
8NK N2    N4  N 0 1 N N N N N N 25.550 13.130 -3.443 -7.074 0.954  -1.661 N2    8NK 27 
8NK N3    N5  N 0 1 N N N N N N 23.532 13.369 -2.361 -4.930 0.514  -0.903 N3    8NK 28 
8NK C4    C11 C 0 1 Y N N N N N 22.982 13.577 -1.155 -4.023 -0.263 -0.300 C4    8NK 29 
8NK H1    H1  H 0 1 N N N N N N 19.122 11.813 3.635  3.071  -1.496 1.657  H1    8NK 30 
8NK H2    H2  H 0 1 N N N N N N 14.454 14.641 3.577  7.146  -2.505 -2.040 H2    8NK 31 
8NK H3    H3  H 0 1 N N N N N N 15.532 11.527 5.058  6.830  0.635  -1.945 H3    8NK 32 
8NK H4    H4  H 0 1 N N N N N N 16.801 13.406 -0.180 1.246  1.094  1.649  H4    8NK 33 
8NK H5    H5  H 0 1 N N N N N N 16.671 11.736 -0.827 2.040  2.530  0.959  H5    8NK 34 
8NK H6    H6  H 0 1 N N N N N N 17.723 13.422 -2.404 0.591  2.278  -1.090 H6    8NK 35 
8NK H7    H7  H 0 1 N N N N N N 18.986 10.842 -1.582 -0.212 3.114  1.590  H7    8NK 36 
8NK H8    H8  H 0 1 N N N N N N 17.464 11.071 -3.332 -1.373 4.711  0.245  H8    8NK 37 
8NK H9    H9  H 0 1 N N N N N N 21.129 11.465 -1.994 -2.040 1.647  1.748  H9    8NK 38 
8NK H10   H10 H 0 1 N N N N N N 21.659 12.546 -3.988 -3.133 3.716  1.125  H10   8NK 39 
8NK H11   H11 H 0 1 N N N N N N 20.633 14.301 -2.616 -2.113 1.436  -1.314 H11   8NK 40 
8NK H12   H12 H 0 1 N N N N N N 20.520 13.953 0.928  -1.287 -1.469 0.964  H12   8NK 41 
8NK H13   H13 H 0 1 N N N N N N 21.901 14.246 2.948  -3.469 -3.314 2.425  H13   8NK 42 
8NK H14   H14 H 0 1 N N N N N N 23.422 13.296 2.866  -3.983 -4.063 0.894  H14   8NK 43 
8NK H15   H15 H 0 1 N N N N N N 23.455 15.070 2.584  -2.251 -3.835 1.236  H15   8NK 44 
8NK H16   H16 H 0 1 N N N N N N 26.580 13.481 -1.246 -7.531 -1.352 -0.706 H16   8NK 45 
8NK H17   H17 H 0 1 N N N N N N 25.067 12.992 -4.308 -7.997 0.677  -1.771 H17   8NK 46 
8NK H18   H18 H 0 1 N N N N N N 26.549 13.109 -3.419 -6.784 1.819  -1.990 H18   8NK 47 
# 
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 
8NK "O2'" "C2'" SING N N 1  
8NK "O3'" "C3'" SING N N 2  
8NK N2    C2    SING N N 3  
8NK "C2'" "C3'" SING N N 4  
8NK "C2'" "C1'" SING N N 5  
8NK N3    C2    DOUB N N 6  
8NK N3    C4    SING N N 7  
8NK C2    N1    SING N N 8  
8NK "C3'" "C4'" SING N N 9  
8NK "C1'" "O4'" SING N N 10 
8NK "C1'" N9    SING N N 11 
8NK "C4'" "O4'" SING N N 12 
8NK "C4'" "C5'" SING N N 13 
8NK N1    C6    SING N N 14 
8NK C4    N9    SING Y N 15 
8NK C4    C5    DOUB Y N 16 
8NK N9    C8    SING Y N 17 
8NK "C5'" "O5'" SING N N 18 
8NK C5    C6    SING N N 19 
8NK C5    N7    SING Y N 20 
8NK C6    O6    DOUB N N 21 
8NK C8    N7    DOUB Y N 22 
8NK "O5'" PA    SING N N 23 
8NK N7    CM7   SING N N 24 
8NK PA    O3A   SING N N 25 
8NK PA    O1A   DOUB N N 26 
8NK PA    O2A   SING N N 27 
8NK O3A   PB    SING N N 28 
8NK O1B   PB    DOUB N N 29 
8NK PB    O2B   SING N N 30 
8NK PB    O3B   SING N N 31 
8NK O2A   H1    SING N N 32 
8NK O2B   H2    SING N N 33 
8NK O3B   H3    SING N N 34 
8NK "C5'" H4    SING N N 35 
8NK "C5'" H5    SING N N 36 
8NK "C4'" H6    SING N N 37 
8NK "C3'" H7    SING N N 38 
8NK "O3'" H8    SING N N 39 
8NK "C2'" H9    SING N N 40 
8NK "O2'" H10   SING N N 41 
8NK "C1'" H11   SING N N 42 
8NK C8    H12   SING N N 43 
8NK CM7   H13   SING N N 44 
8NK CM7   H14   SING N N 45 
8NK CM7   H15   SING N N 46 
8NK N1    H16   SING N N 47 
8NK N2    H17   SING N N 48 
8NK N2    H18   SING N N 49 
# 
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 
8NK InChI            InChI                1.03  "InChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1" 
8NK InChIKey         InChI                1.03  SBASPRRECYVBRF-KQYNXXCUSA-O                                                                                                                                                                         
8NK SMILES_CANONICAL CACTVS               3.385 "C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13"                                                                                                                
8NK SMILES           CACTVS               3.385 "C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13"                                                                                                                      
8NK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                  
8NK SMILES           "OpenEye OEToolkits" 2.0.6 "C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           8NK 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.6 
_pdbx_chem_comp_identifier.identifier        "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
8NK "Create component"   2017-02-13 EBI  
8NK "Initial release"    2017-05-24 RCSB 
8NK "Obsolete component" 2024-02-25 RCSB 
# 
