data_JYP
#

_chem_comp.id                                   JYP
_chem_comp.name                                 "Adenophostin A"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H26 N5 O18 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-10-23
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       669.322
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    JYP
_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       6MU1
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
JYP  C1   C1   C  0  1  Y  N  N  181.515  139.482  87.801   7.494  -0.910  -0.448  C1   JYP   1  
JYP  N1   N1   N  0  1  Y  N  N  181.775  140.819  87.672   6.304  -0.424  -0.729  N1   JYP   2  
JYP  C2   C2   C  0  1  Y  N  N  180.826  141.696  88.010   5.751   0.505   0.045  C2   JYP   3  
JYP  C3   C3   C  0  1  Y  N  N  179.573  141.257  88.502   6.457   0.963   1.171  C3   JYP   4  
JYP  C4   C4   C  0  1  Y  N  N  179.362  139.924  88.618   7.724   0.414   1.428  C4   JYP   5  
JYP  N2   N2   N  0  1  Y  N  N  180.321  139.066  88.286   8.194  -0.511   0.598  N2   JYP   6  
JYP  N3   N3   N  0  1  N  N  N  178.142  139.435  89.262   8.466   0.826   2.522  N3   JYP   7  
JYP  N4   N4   N  0  1  Y  N  N  178.676  142.512  88.575   5.680   1.893   1.777  N4   JYP   8  
JYP  C5   C5   C  0  1  Y  N  N  179.528  143.501  88.124   4.571   2.032   1.111  C5   JYP   9  
JYP  N5   N5   N  0  1  Y  N  N  180.663  142.950  87.840   4.567   1.197   0.034  N5   JYP  10  
JYP  C6   C6   C  0  1  N  N  R  181.524  143.623  86.892   3.494   1.062  -0.955  C6   JYP  11  
JYP  C7   C7   C  0  1  N  N  R  181.540  145.085  87.179   2.513  -0.054  -0.535  C7   JYP  12  
JYP  C8   C8   C  0  1  N  N  S  182.915  145.475  87.453   1.128   0.484  -0.958  C8   JYP  13  
JYP  C9   C9   C  0  1  N  N  R  183.768  144.256  87.353   1.436   1.863  -1.583  C9   JYP  14  
JYP  O1   O1   O  0  1  N  N  N  182.899  143.111  87.018   2.692   2.263  -0.993  O1   JYP  15  
JYP  C10  C10  C  0  1  N  N  N  184.450  144.005  88.667   0.337   2.867  -1.228  C10  JYP  16  
JYP  O2   O2   O  0  1  N  N  N  185.060  142.723  88.646   0.580   4.099  -1.909  O2   JYP  17  
JYP  O3   O3   O  0  1  N  N  N  183.007  146.031  88.801   0.278   0.630   0.182  O3   JYP  18  
JYP  C11  C11  C  0  1  N  N  R  182.980  147.455  88.733  -1.112   0.456  -0.103  C11  JYP  19  
JYP  C12  C12  C  0  1  N  N  S  184.260  148.010  89.329  -1.939   0.874   1.115  C12  JYP  20  
JYP  C13  C13  C  0  1  N  N  R  184.025  148.394  90.807  -3.422   0.628   0.824  C13  JYP  21  
JYP  C14  C14  C  0  1  N  N  S  182.985  149.503  90.892  -3.623  -0.847   0.464  C14  JYP  22  
JYP  C15  C15  C  0  1  N  N  S  181.929  149.297  89.812  -2.730  -1.200  -0.729  C15  JYP  23  
JYP  O4   O4   O  0  1  N  N  N  181.879  147.933  89.449  -1.368  -0.918  -0.402  O4   JYP  24  
JYP  C16  C16  C  0  1  N  N  N  180.558  149.730  90.350  -2.880  -2.687  -1.056  C16  JYP  25  
JYP  O5   O5   O  0  1  N  N  N  180.272  151.030  89.913  -2.138  -2.991  -2.239  O5   JYP  26  
JYP  O6   O6   O  0  1  N  N  N  183.613  150.746  90.701  -4.991  -1.074   0.122  O6   JYP  27  
JYP  P1   P1   P  0  1  N  N  N  183.504  151.889  91.921  -5.936  -2.105   0.919  P1   JYP  28  
JYP  O7   O7   O  0  1  N  N  N  183.324  151.193  93.249  -7.365  -2.203   0.184  O7   JYP  29  
JYP  O8   O8   O  0  1  N  N  N  182.317  152.793  91.662  -5.300  -3.441   0.942  O8   JYP  30  
JYP  O9   O9   O  0  1  N  N  N  184.771  152.717  91.953  -6.144  -1.584   2.429  O9   JYP  31  
JYP  O10  O10  O  0  1  N  N  N  185.221  148.841  91.364  -3.837   1.447  -0.271  O10  JYP  32  
JYP  P2   P2   P  0  1  N  N  N  185.316  148.991  93.006  -5.004   2.550  -0.149  P2   JYP  33  
JYP  O11  O11  O  0  1  N  N  N  185.970  147.761  93.586  -5.115   3.370  -1.530  O11  JYP  34  
JYP  O12  O12  O  0  1  N  N  N  183.930  149.141  93.580  -6.405   1.817   0.154  O12  JYP  35  
JYP  O13  O13  O  0  1  N  N  N  186.139  150.212  93.354  -4.687   3.483   0.955  O13  JYP  36  
JYP  O14  O14  O  0  1  N  N  N  184.650  149.142  88.614  -1.729   2.263   1.380  O14  JYP  37  
JYP  O15  O15  O  0  1  N  N  N  181.041  145.823  86.018   2.810  -1.269  -1.227  O15  JYP  38  
JYP  P3   P3   P  0  1  N  N  N  182.102  146.817  85.186   3.174  -2.642  -0.471  P3   JYP  39  
JYP  O16  O16  O  0  1  N  N  N  183.110  147.404  86.151   4.564  -2.466   0.323  O16  JYP  40  
JYP  O17  O17  O  0  1  N  N  N  182.825  146.012  84.131   2.098  -2.979   0.487  O17  JYP  41  
JYP  O18  O18  O  0  1  N  N  N  181.325  147.940  84.521   3.321  -3.827  -1.552  O18  JYP  42  
JYP  H1   H1   H  0  1  N  N  N  182.263  138.757  87.516   7.912  -1.667  -1.096  H1   JYP  43  
JYP  H2   H2   H  0  1  N  N  N  178.199  138.443  89.374   8.111   1.502   3.121  H2   JYP  44  
JYP  H3   H3   H  0  1  N  N  N  178.042  139.867  90.158   9.340   0.440   2.689  H3   JYP  45  
JYP  H4   H4   H  0  1  N  N  N  179.289  144.550  88.026   3.771   2.709   1.373  H4   JYP  46  
JYP  H5   H5   H  0  1  N  N  N  181.160  143.456  85.868   3.909   0.852  -1.940  H5   JYP  47  
JYP  H6   H6   H  0  1  N  N  N  180.908  145.294  88.055   2.549  -0.210   0.543  H6   JYP  48  
JYP  H7   H7   H  0  1  N  N  N  183.250  146.220  86.716   0.669  -0.177  -1.693  H7   JYP  49  
JYP  H8   H8   H  0  1  N  N  N  184.524  144.396  86.566   1.534   1.776  -2.665  H8   JYP  50  
JYP  H9   H9   H  0  1  N  N  N  185.218  144.774  88.834  -0.631   2.468  -1.531  H9   JYP  51  
JYP  H10  H10  H  0  1  N  N  N  183.709  144.045  89.479   0.338   3.040  -0.152  H10  JYP  52  
JYP  H11  H11  H  0  1  N  N  N  185.492  142.564  89.477  -0.079   4.784  -1.730  H11  JYP  53  
JYP  H12  H12  H  0  1  N  N  N  182.917  147.775  87.683  -1.387   1.072  -0.959  H12  JYP  54  
JYP  H13  H13  H  0  1  N  N  N  185.040  147.235  89.287  -1.635   0.287   1.981  H13  JYP  55  
JYP  H14  H14  H  0  1  N  N  N  183.650  147.511  91.345  -4.013   0.872   1.707  H14  JYP  56  
JYP  H15  H15  H  0  1  N  N  N  182.499  149.462  91.878  -3.353  -1.470   1.317  H15  JYP  57  
JYP  H16  H16  H  0  1  N  N  N  182.182  149.919  88.941  -3.027  -0.606  -1.593  H16  JYP  58  
JYP  H17  H17  H  0  1  N  N  N  179.785  149.041  89.980  -2.499  -3.282  -0.226  H17  JYP  59  
JYP  H18  H18  H  0  1  N  N  N  180.572  149.708  91.450  -3.932  -2.920  -1.217  H18  JYP  60  
JYP  H19  H19  H  0  1  N  N  N  179.423  151.297  90.246  -2.187  -3.919  -2.507  H19  JYP  61  
JYP  H20  H20  H  0  1  N  N  N  182.504  151.468  93.643  -7.987  -2.807   0.612  H20  JYP  62  
JYP  H21  H21  H  0  1  N  N  N  184.557  153.630  91.804  -6.557  -0.712   2.491  H21  JYP  63  
JYP  H22  H22  H  0  1  N  N  N  186.762  148.011  94.048  -5.800   4.052  -1.528  H22  JYP  64  
JYP  H23  H23  H  0  1  N  N  N  183.865  149.970  94.039  -6.677   1.189  -0.529  H23  JYP  65  
JYP  H24  H24  H  0  1  N  N  N  185.452  149.491  88.986  -0.808   2.492   1.569  H24  JYP  66  
JYP  H25  H25  H  0  1  N  N  N  183.986  147.144  85.892   5.315  -2.244  -0.244  H25  JYP  67  
JYP  H26  H26  H  0  1  N  N  N  181.455  147.902  83.581   3.540  -4.686  -1.166  H26  JYP  68  
#   #
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
JYP  O17  P3   DOUB  N  N   1  
JYP  O18  P3   SING  N  N   2  
JYP  P3   O15  SING  N  N   3  
JYP  P3   O16  SING  N  N   4  
JYP  O15  C7   SING  N  N   5  
JYP  C6   O1   SING  N  N   6  
JYP  C6   C7   SING  N  N   7  
JYP  C6   N5   SING  N  N   8  
JYP  O1   C9   SING  N  N   9  
JYP  C7   C8   SING  N  N  10  
JYP  C9   C8   SING  N  N  11  
JYP  C9   C10  SING  N  N  12  
JYP  C8   O3   SING  N  N  13  
JYP  N1   C1   DOUB  Y  N  14  
JYP  N1   C2   SING  Y  N  15  
JYP  C1   N2   SING  Y  N  16  
JYP  N5   C2   SING  Y  N  17  
JYP  N5   C5   SING  Y  N  18  
JYP  C2   C3   DOUB  Y  N  19  
JYP  C5   N4   DOUB  Y  N  20  
JYP  N2   C4   DOUB  Y  N  21  
JYP  C3   N4   SING  Y  N  22  
JYP  C3   C4   SING  Y  N  23  
JYP  O14  C12  SING  N  N  24  
JYP  C4   N3   SING  N  N  25  
JYP  O2   C10  SING  N  N  26  
JYP  C11  O3   SING  N  N  27  
JYP  C11  C12  SING  N  N  28  
JYP  C11  O4   SING  N  N  29  
JYP  C12  C13  SING  N  N  30  
JYP  O4   C15  SING  N  N  31  
JYP  C15  C16  SING  N  N  32  
JYP  C15  C14  SING  N  N  33  
JYP  O5   C16  SING  N  N  34  
JYP  O6   C14  SING  N  N  35  
JYP  O6   P1   SING  N  N  36  
JYP  C13  C14  SING  N  N  37  
JYP  C13  O10  SING  N  N  38  
JYP  O10  P2   SING  N  N  39  
JYP  O8   P1   DOUB  N  N  40  
JYP  P1   O9   SING  N  N  41  
JYP  P1   O7   SING  N  N  42  
JYP  P2   O13  DOUB  N  N  43  
JYP  P2   O12  SING  N  N  44  
JYP  P2   O11  SING  N  N  45  
JYP  C1   H1   SING  N  N  46  
JYP  N3   H2   SING  N  N  47  
JYP  N3   H3   SING  N  N  48  
JYP  C5   H4   SING  N  N  49  
JYP  C6   H5   SING  N  N  50  
JYP  C7   H6   SING  N  N  51  
JYP  C8   H7   SING  N  N  52  
JYP  C9   H8   SING  N  N  53  
JYP  C10  H9   SING  N  N  54  
JYP  C10  H10  SING  N  N  55  
JYP  O2   H11  SING  N  N  56  
JYP  C11  H12  SING  N  N  57  
JYP  C12  H13  SING  N  N  58  
JYP  C13  H14  SING  N  N  59  
JYP  C14  H15  SING  N  N  60  
JYP  C15  H16  SING  N  N  61  
JYP  C16  H17  SING  N  N  62  
JYP  C16  H18  SING  N  N  63  
JYP  O5   H19  SING  N  N  64  
JYP  O7   H20  SING  N  N  65  
JYP  O9   H21  SING  N  N  66  
JYP  O11  H22  SING  N  N  67  
JYP  O12  H23  SING  N  N  68  
JYP  O14  H24  SING  N  N  69  
JYP  O16  H25  SING  N  N  70  
JYP  O18  H26  SING  N  N  71  
#   #
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
JYP  InChI             InChI                 1.03   "InChI=1S/C16H26N5O18P3/c17-13-7-14(19-3-18-13)21(4-20-7)15-12(39-42(31,32)33)9(5(1-22)34-15)36-16-8(24)11(38-41(28,29)30)10(6(2-23)35-16)37-40(25,26)27/h3-6,8-12,15-16,22-24H,1-2H2,(H2,17,18,19)(H2,25,26,27)(H2,28,29,30)(H2,31,32,33)/t5-,6+,8+,9+,10+,11-,12-,15-,16-/m1/s1"  
JYP  InChIKey          InChI                 1.03   RENVITLQVBEFDT-YFPOSXHWSA-N  
JYP  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O[C@H]4O[C@@H](CO)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H]4O)[C@H]3O[P](O)(O)=O"  
JYP  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[CH]4O[CH](CO)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]4O)[CH]3O[P](O)(O)=O"  
JYP  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)CO)O[C@@H]4[C@H]([C@H]([C@H]([C@@H](O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N"  
JYP  SMILES            "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OC4C(C(C(C(O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N"  
#
_pdbx_chem_comp_identifier.comp_id          JYP
_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~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen 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
JYP  "Create component"  2018-10-23  RCSB  
JYP  "Initial release"   2018-12-05  RCSB  
JYP  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     JYP
_pdbx_chem_comp_synonyms.name        "[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
