data_6AD
#

_chem_comp.id                                   6AD
_chem_comp.name                                 "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H17 N5 O10 P2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2-methylthio-adenosine-5'-diphosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-03-31
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       473.293
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    6AD
_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       4PXZ
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
6AD  O2B    O2B    O  0  1  N  N  N  16.181   1.025  59.445  -6.634   2.036  -2.191  O2B    6AD   1  
6AD  PB     PB     P  0  1  N  N  N  16.569   0.984  57.870  -6.253   1.557  -0.702  PB     6AD   2  
6AD  O3B    O3B    O  0  1  N  N  N  18.003   0.277  57.772  -5.854   2.838   0.188  O3B    6AD   3  
6AD  O1B    O1B    O  0  1  N  N  N  16.571   2.339  57.263  -7.416   0.875  -0.091  O1B    6AD   4  
6AD  O3A    O3A    O  0  1  N  N  N  15.481  -0.035  57.297  -5.008   0.539  -0.767  O3A    6AD   5  
6AD  PA     PA     P  0  1  N  N  N  15.599  -0.994  55.991  -4.418  -0.573   0.237  PA     6AD   6  
6AD  O2A    O2A    O  0  1  N  N  N  15.940  -2.388  56.356  -5.290  -1.921   0.116  O2A    6AD   7  
6AD  O1A    O1A    O  0  1  N  N  N  16.343  -0.306  54.904  -4.483  -0.067   1.627  O1A    6AD   8  
6AD  "O5'"  "O5'"  O  0  1  N  N  N  14.034  -1.053  55.675  -2.887  -0.887  -0.149  "O5'"  6AD   9  
6AD  "C5'"  "C5'"  C  0  1  N  N  N  13.267   0.075  55.188  -2.053  -1.755   0.621  "C5'"  6AD  10  
6AD  "C4'"  "C4'"  C  0  1  N  N  R  11.889  -0.406  54.659  -0.666  -1.831  -0.021  "C4'"  6AD  11  
6AD  "O4'"  "O4'"  O  0  1  N  N  N  12.011  -1.113  53.382   0.028  -0.574   0.131  "O4'"  6AD  12  
6AD  "C3'"  "C3'"  C  0  1  N  N  S  11.197  -1.374  55.631   0.214  -2.861   0.721  "C3'"  6AD  13  
6AD  "O3'"  "O3'"  O  0  1  N  N  N   9.769  -1.226  55.606   0.219  -4.109   0.026  "O3'"  6AD  14  
6AD  "C2'"  "C2'"  C  0  1  N  N  R  11.582  -2.723  55.107   1.623  -2.227   0.710  "C2'"  6AD  15  
6AD  "O2'"  "O2'"  O  0  1  N  N  N  10.634  -3.727  55.422   2.543  -3.063   0.006  "O2'"  6AD  16  
6AD  "C1'"  "C1'"  C  0  1  N  N  R  11.687  -2.525  53.603   1.427  -0.889  -0.038  "C1'"  6AD  17  
6AD  N9     N9     N  0  1  Y  N  N  12.703  -3.449  53.002   2.261   0.156   0.561  N9     6AD  18  
6AD  C8     C8     C  0  1  Y  N  N  13.886  -3.813  53.502   1.889   1.018   1.551  C8     6AD  19  
6AD  N7     N7     N  0  1  Y  N  N  14.434  -4.713  52.697   2.876   1.814   1.841  N7     6AD  20  
6AD  C5     C5     C  0  1  Y  N  N  13.612  -4.895  51.659   3.942   1.516   1.058  C5     6AD  21  
6AD  C4     C4     C  0  1  Y  N  N  12.518  -4.136  51.880   3.561   0.445   0.231  C4     6AD  22  
6AD  N3     N3     N  0  1  Y  N  N  11.505  -4.135  50.996   4.437  -0.043  -0.641  N3     6AD  23  
6AD  C2     C2     C  0  1  Y  N  N  11.566  -4.903  49.892   5.654   0.471  -0.732  C2     6AD  24  
6AD  S1     S1     S  0  1  N  N  N  10.191  -4.864  48.788   6.780  -0.210  -1.904  S1     6AD  25  
6AD  C11    C11    C  0  1  N  N  N  10.293  -6.409  47.909   8.223   0.839  -1.600  C11    6AD  26  
6AD  N1     N1     N  0  1  Y  N  N  12.677  -5.636  49.644   6.055   1.483   0.028  N1     6AD  27  
6AD  C6     C6     C  0  1  Y  N  N  13.688  -5.642  50.532   5.246   2.024   0.932  C6     6AD  28  
6AD  N6     N6     N  0  1  N  N  N  14.761  -6.416  50.348   5.672   3.079   1.720  N6     6AD  29  
6AD  H1     H1     H  0  1  N  N  N  16.020   1.923  59.709  -7.378   2.652  -2.228  H1     6AD  30  
6AD  H2     H2     H  0  1  N  N  N  18.614   0.859  57.335  -5.098   3.334  -0.154  H2     6AD  31  
6AD  H3     H3     H  0  1  N  N  N  16.650  -2.695  55.805  -5.293  -2.309  -0.769  H3     6AD  32  
6AD  H4     H4     H  0  1  N  N  N  13.819   0.565  54.373  -1.963  -1.367   1.635  H4     6AD  33  
6AD  H5     H5     H  0  1  N  N  N  13.112   0.791  56.008  -2.495  -2.751   0.650  H5     6AD  34  
6AD  H6     H6     H  0  1  N  N  N  11.244   0.475  54.528  -0.751  -2.095  -1.076  H6     6AD  35  
6AD  H7     H7     H  0  1  N  N  N  11.595  -1.230  56.646  -0.136  -2.996   1.744  H7     6AD  36  
6AD  H8     H8     H  0  1  N  N  N   9.376  -1.838  56.217   0.757  -4.793   0.449  H8     6AD  37  
6AD  H9     H9     H  0  1  N  N  N  12.572  -2.995  55.501   1.971  -2.050   1.728  H9     6AD  38  
6AD  H10    H10    H  0  1  N  N  N  10.586  -3.833  56.365   2.658  -3.939   0.400  H10    6AD  39  
6AD  H11    H11    H  0  1  N  N  N  10.706  -2.743  53.156   1.665  -1.007  -1.095  H11    6AD  40  
6AD  H12    H12    H  0  1  N  N  N  14.325  -3.436  54.414   0.918   1.036   2.024  H12    6AD  41  
6AD  H13    H13    H  0  1  N  N  N   9.465  -6.476  47.188   9.035   0.540  -2.264  H13    6AD  42  
6AD  H14    H14    H  0  1  N  N  N  11.252  -6.463  47.373   7.962   1.880  -1.790  H14    6AD  43  
6AD  H15    H15    H  0  1  N  N  N  10.225  -7.242  48.624   8.541   0.727  -0.564  H15    6AD  44  
6AD  H16    H16    H  0  1  N  N  N  14.658  -6.933  49.498   6.570   3.430   1.615  H16    6AD  45  
6AD  H17    H17    H  0  1  N  N  N  15.579  -5.844  50.293   5.073   3.467   2.377  H17    6AD  46  
#   #
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
6AD  C11    S1     SING  N  N   1  
6AD  S1     C2     SING  N  N   2  
6AD  N1     C2     DOUB  Y  N   3  
6AD  N1     C6     SING  Y  N   4  
6AD  C2     N3     SING  Y  N   5  
6AD  N6     C6     SING  N  N   6  
6AD  C6     C5     DOUB  Y  N   7  
6AD  N3     C4     DOUB  Y  N   8  
6AD  C5     C4     SING  Y  N   9  
6AD  C5     N7     SING  Y  N  10  
6AD  C4     N9     SING  Y  N  11  
6AD  N7     C8     DOUB  Y  N  12  
6AD  N9     C8     SING  Y  N  13  
6AD  N9     "C1'"  SING  N  N  14  
6AD  "O4'"  "C1'"  SING  N  N  15  
6AD  "O4'"  "C4'"  SING  N  N  16  
6AD  "C1'"  "C2'"  SING  N  N  17  
6AD  "C4'"  "C5'"  SING  N  N  18  
6AD  "C4'"  "C3'"  SING  N  N  19  
6AD  O1A    PA     DOUB  N  N  20  
6AD  "C2'"  "O2'"  SING  N  N  21  
6AD  "C2'"  "C3'"  SING  N  N  22  
6AD  "C5'"  "O5'"  SING  N  N  23  
6AD  "O3'"  "C3'"  SING  N  N  24  
6AD  "O5'"  PA     SING  N  N  25  
6AD  PA     O2A    SING  N  N  26  
6AD  PA     O3A    SING  N  N  27  
6AD  O1B    PB     DOUB  N  N  28  
6AD  O3A    PB     SING  N  N  29  
6AD  O3B    PB     SING  N  N  30  
6AD  PB     O2B    SING  N  N  31  
6AD  O2B    H1     SING  N  N  32  
6AD  O3B    H2     SING  N  N  33  
6AD  O2A    H3     SING  N  N  34  
6AD  "C5'"  H4     SING  N  N  35  
6AD  "C5'"  H5     SING  N  N  36  
6AD  "C4'"  H6     SING  N  N  37  
6AD  "C3'"  H7     SING  N  N  38  
6AD  "O3'"  H8     SING  N  N  39  
6AD  "C2'"  H9     SING  N  N  40  
6AD  "O2'"  H10    SING  N  N  41  
6AD  "C1'"  H11    SING  N  N  42  
6AD  C8     H12    SING  N  N  43  
6AD  C11    H13    SING  N  N  44  
6AD  C11    H14    SING  N  N  45  
6AD  C11    H15    SING  N  N  46  
6AD  N6     H16    SING  N  N  47  
6AD  N6     H17    SING  N  N  48  
#   #
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
6AD  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(nc(SC)nc12)N)C(O)C3O"  
6AD  InChI             InChI                 1.03   "InChI=1S/C11H17N5O10P2S/c1-29-11-14-8(12)5-9(15-11)16(3-13-5)10-7(18)6(17)4(25-10)2-24-28(22,23)26-27(19,20)21/h3-4,6-7,10,17-18H,2H2,1H3,(H,22,23)(H2,12,14,15)(H2,19,20,21)/t4-,6-,7-,10-/m1/s1"  
6AD  InChIKey          InChI                 1.03   WLMZTKAZJUWXCB-KQYNXXCUSA-N  
6AD  SMILES_CANONICAL  CACTVS                3.385  "CSc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1"  
6AD  SMILES            CACTVS                3.385  "CSc1nc(N)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)c2n1"  
6AD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O)N"  
6AD  SMILES            "OpenEye OEToolkits"  1.7.6  "CSc1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
6AD  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)"  
6AD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-5-(6-azanyl-2-methylsulfanyl-purin-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
6AD  "Create component"  2014-03-31  PDBJ  
6AD  "Initial release"   2014-04-30  RCSB  
6AD  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     6AD
_pdbx_chem_comp_synonyms.name        "2-methylthio-adenosine-5'-diphosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
