data_365
#

_chem_comp.id                                   365
_chem_comp.name                                 "[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H27 B N6 O10 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine"
_chem_comp.pdbx_formal_charge                   -1
_chem_comp.pdbx_initial_date                    2013-01-21
_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                       565.258
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    365
_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       3ZJV
_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.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
365  O3P     O3P     O   0  1  N  N  N  52.194  -19.417  30.287   6.479   1.104  -1.806  O3P     365   1  
365  B       B       B  -1  1  N  N  N  53.697  -26.635  32.889  -1.304   1.454   1.095  B       365   2  
365  P       P       P   0  1  N  N  N  51.652  -20.043  31.671   5.709   1.563  -0.468  P       365   3  
365  N1      N1      N   0  1  Y  N  N  57.039  -22.030  26.320  -2.136  -5.651   0.366  N1      365   4  
365  O1      O1      O   0  1  N  N  N  54.570  -27.553  33.535  -1.603   1.673   2.415  O1      365   5  
365  C2      C2      C   0  1  Y  N  N  55.964  -22.845  26.292  -2.492  -4.477  -0.121  C2      365   6  
365  N3      N3      N   0  1  Y  N  N  55.445  -23.400  27.398  -1.690  -3.432  -0.104  N3      365   7  
365  C4      C4      C   0  1  Y  N  N  56.037  -23.126  28.575  -0.470  -3.524   0.414  C4      365   8  
365  C5      C5      C   0  1  Y  N  N  57.126  -22.269  28.639  -0.044  -4.754   0.945  C5      365   9  
365  C6      C6      C   0  1  Y  N  N  57.637  -21.722  27.483  -0.936  -5.839   0.904  C6      365  10  
365  N6      N6      N   0  1  N  N  N  58.703  -20.885  27.534  -0.572  -7.074   1.412  N6      365  11  
365  N7      N7      N   0  1  Y  N  N  57.497  -22.159  29.924   1.219  -4.576   1.401  N7      365  12  
365  C8      C8      C   0  1  Y  N  N  56.653  -22.936  30.630   1.587  -3.345   1.189  C8      365  13  
365  N9      N9      N   0  1  Y  N  N  55.763  -23.527  29.810   0.579  -2.656   0.582  N9      365  14  
365  "C1'"   "C1'"   C   0  1  N  N  R  54.674  -24.482  30.138   0.611  -1.247   0.182  "C1'"   365  15  
365  C10     C10     C   0  1  N  N  S  53.991  -28.840  33.790  -2.296   2.934   2.459  C10     365  16  
365  C11     C11     C   0  1  Y  N  N  52.584  -28.641  33.416  -2.996   3.088   1.130  C11     365  17  
365  C12     C12     C   0  1  Y  N  N  52.398  -27.336  32.826  -2.396   2.183   0.264  C12     365  18  
365  C13     C13     C   0  1  Y  N  N  51.546  -29.551  33.528  -4.022   3.892   0.686  C13     365  19  
365  C14     C14     C   0  1  Y  N  N  50.284  -29.169  33.091  -4.454   3.802  -0.626  C14     365  20  
365  C15     C15     C   0  1  Y  N  N  50.072  -27.911  32.528  -3.857   2.906  -1.492  C15     365  21  
365  C16     C16     C   0  1  Y  N  N  51.125  -26.981  32.397  -2.824   2.093  -1.047  C16     365  22  
365  C17     C17     C   0  1  N  N  N  54.587  -29.883  32.860  -3.321   2.930   3.594  C17     365  23  
365  N18     N18     N   0  1  N  N  N  54.607  -29.409  31.469  -2.622   2.866   4.885  N18     365  24  
365  O19     O19     O   0  1  N  N  N  50.868  -25.755  31.841  -2.235   1.212  -1.898  O19     365  25  
365  O1P     O1P     O   0  1  N  N  N  52.513  -19.439  32.740   6.372   0.966   0.712  O1P     365  26  
365  "C2'"   "C2'"   C   0  1  N  N  R  54.943  -25.244  31.416  -0.014  -0.363   1.282  "C2'"   365  27  
365  "O2'"   "O2'"   O   0  1  N  N  N  54.180  -26.467  31.561  -1.299   0.109   0.819  "O2'"   365  28  
365  C20     C20     C   0  1  N  N  N  49.512  -25.301  31.752  -2.729   1.174  -3.238  C20     365  29  
365  C21     C21     C   0  1  N  N  N  49.453  -24.005  30.973  -1.950   0.130  -4.040  C21     365  30  
365  C22     C22     C   0  1  N  N  N  48.837  -24.266  29.609  -2.479   0.090  -5.475  C22     365  31  
365  O23     O23     O   0  1  N  N  N  48.022  -23.144  29.267  -1.751  -0.885  -6.224  O23     365  32  
365  O2P     O2P     O   0  1  N  N  N  50.140  -19.839  31.736   5.748   3.168  -0.352  O2P     365  33  
365  "C3'"   "C3'"   C   0  1  N  N  S  54.351  -24.365  32.467   0.861   0.925   1.265  "C3'"   365  34  
365  "O3'"   "O3'"   O   0  1  N  N  N  53.837  -25.300  33.386  -0.055   1.938   0.795  "O3'"   365  35  
365  "C4'"   "C4'"   C   0  1  N  N  R  53.254  -23.595  31.751   1.901   0.650   0.158  "C4'"   365  36  
365  "O4'"   "O4'"   O   0  1  N  N  N  53.426  -23.839  30.342   1.975  -0.789   0.067  "O4'"   365  37  
365  "C5'"   "C5'"   C   0  1  N  N  N  53.253  -22.103  31.974   3.262   1.229   0.551  "C5'"   365  38  
365  "O5'"   "O5'"   O   0  1  N  N  N  52.035  -21.568  31.425   4.179   1.067  -0.533  "O5'"   365  39  
365  H2      H2      H   0  1  N  N  N  55.502  -23.060  25.340  -3.477  -4.368  -0.550  H2      365  40  
365  HN6     HN6     H   0  1  N  N  N  58.928  -20.575  26.610  -1.197  -7.815   1.377  HN6     365  41  
365  HN6A    HN6A    H   0  0  N  N  N  58.480  -20.095  28.105   0.307  -7.198   1.802  HN6A    365  42  
365  H8      H8      H   0  1  N  N  N  56.685  -23.067  31.702   2.548  -2.931   1.455  H8      365  43  
365  "H1'"   "H1'"   H   0  1  N  N  N  54.584  -25.208  29.316   0.082  -1.110  -0.761  "H1'"   365  44  
365  H10     H10     H   0  1  N  N  N  54.095  -29.144  34.842  -1.583   3.746   2.602  H10     365  45  
365  H13     H13     H   0  1  N  N  N  51.714  -30.533  33.945  -4.490   4.593   1.362  H13     365  46  
365  H14     H14     H   0  1  N  N  N  49.456  -29.855  33.189  -5.259   4.433  -0.973  H14     365  47  
365  H15     H15     H   0  1  N  N  N  49.083  -27.643  32.186  -4.195   2.839  -2.516  H15     365  48  
365  H17     H17     H   0  1  N  N  N  55.617  -30.101  33.179  -3.918   3.841   3.549  H17     365  49  
365  H17A    H17A    H   0  0  N  N  N  53.983  -30.801  32.917  -3.974   2.062   3.491  H17A    365  50  
365  HN18    HN18    H   0  0  N  N  N  55.003  -30.115  30.882  -1.963   3.624   4.977  HN18    365  51  
365  HN1A    HN1A    H   0  0  N  N  N  53.673  -29.213  31.170  -3.279   2.862   5.652  HN1A    365  52  
365  "H2'"   "H2'"   H   0  1  N  N  N  56.021  -25.399  31.573  -0.062  -0.856   2.253  "H2'"   365  53  
365  H20     H20     H   0  1  N  N  N  48.905  -26.062  31.240  -3.787   0.909  -3.228  H20     365  54  
365  H20A    H20A    H   0  0  N  N  N  49.115  -25.136  32.765  -2.605   2.154  -3.699  H20A    365  55  
365  H21     H21     H   0  1  N  N  N  48.838  -23.275  31.520  -0.892   0.395  -4.050  H21     365  56  
365  H21A    H21A    H   0  0  N  N  N  50.470  -23.606  30.846  -2.074  -0.850  -3.579  H21A    365  57  
365  H22     H22     H   0  1  N  N  N  49.632  -24.392  28.859  -3.536  -0.175  -5.465  H22     365  58  
365  H22A    H22A    H   0  0  N  N  N  48.221  -25.177  29.646  -2.355   1.070  -5.936  H22A    365  59  
365  HO23    HO23    H   0  0  N  N  N  47.626  -23.287  28.415  -2.034  -0.965  -7.145  HO23    365  60  
365  "H3'"   "H3'"   H   0  1  N  N  N  55.099  -23.688  32.906   1.302   1.162   2.234  "H3'"   365  61  
365  "H4'"   "H4'"   H   0  1  N  N  N  52.282  -23.996  32.075   1.567   1.074  -0.789  "H4'"   365  62  
365  "H5'"   "H5'"   H   0  1  N  N  N  53.302  -21.887  33.052   3.154   2.289   0.780  "H5'"   365  63  
365  "H5'A"  "H5'A"  H   0  0  N  N  N  54.119  -21.650  31.470   3.640   0.705   1.429  "H5'A"  365  64  
365  HOP3    HOP3    H   0  0  N  N  N  52.915  -18.826  30.467   7.409   1.370  -1.836  HOP3    365  65  
365  HOP2    HOP2    H   0  0  N  N  N  49.923  -19.318  32.500   5.330   3.627  -1.093  HOP2    365  66  
#   #
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
365  O3P    P       SING  N  N   1  
365  B      O1      SING  N  N   2  
365  B      C12     SING  N  N   3  
365  B      "O2'"   SING  N  N   4  
365  B      "O3'"   SING  N  N   5  
365  P      O1P     DOUB  N  N   6  
365  P      O2P     SING  N  N   7  
365  P      "O5'"   SING  N  N   8  
365  N1     C2      DOUB  Y  N   9  
365  N1     C6      SING  Y  N  10  
365  O1     C10     SING  N  N  11  
365  C2     N3      SING  Y  N  12  
365  N3     C4      DOUB  Y  N  13  
365  C4     C5      SING  Y  N  14  
365  C4     N9      SING  Y  N  15  
365  C5     C6      DOUB  Y  N  16  
365  C5     N7      SING  Y  N  17  
365  C6     N6      SING  N  N  18  
365  N7     C8      DOUB  Y  N  19  
365  C8     N9      SING  Y  N  20  
365  N9     "C1'"   SING  N  N  21  
365  "C1'"  "C2'"   SING  N  N  22  
365  "C1'"  "O4'"   SING  N  N  23  
365  C10    C11     SING  N  N  24  
365  C10    C17     SING  N  N  25  
365  C11    C12     DOUB  Y  N  26  
365  C11    C13     SING  Y  N  27  
365  C12    C16     SING  Y  N  28  
365  C13    C14     DOUB  Y  N  29  
365  C14    C15     SING  Y  N  30  
365  C15    C16     DOUB  Y  N  31  
365  C16    O19     SING  N  N  32  
365  C17    N18     SING  N  N  33  
365  O19    C20     SING  N  N  34  
365  "C2'"  "O2'"   SING  N  N  35  
365  "C2'"  "C3'"   SING  N  N  36  
365  C20    C21     SING  N  N  37  
365  C21    C22     SING  N  N  38  
365  C22    O23     SING  N  N  39  
365  "C3'"  "O3'"   SING  N  N  40  
365  "C3'"  "C4'"   SING  N  N  41  
365  "C4'"  "O4'"   SING  N  N  42  
365  "C4'"  "C5'"   SING  N  N  43  
365  "C5'"  "O5'"   SING  N  N  44  
365  C2     H2      SING  N  N  45  
365  N6     HN6     SING  N  N  46  
365  N6     HN6A    SING  N  N  47  
365  C8     H8      SING  N  N  48  
365  "C1'"  "H1'"   SING  N  N  49  
365  C10    H10     SING  N  N  50  
365  C13    H13     SING  N  N  51  
365  C14    H14     SING  N  N  52  
365  C15    H15     SING  N  N  53  
365  C17    H17     SING  N  N  54  
365  C17    H17A    SING  N  N  55  
365  N18    HN18    SING  N  N  56  
365  N18    HN1A    SING  N  N  57  
365  "C2'"  "H2'"   SING  N  N  58  
365  C20    H20     SING  N  N  59  
365  C20    H20A    SING  N  N  60  
365  C21    H21     SING  N  N  61  
365  C21    H21A    SING  N  N  62  
365  C22    H22     SING  N  N  63  
365  C22    H22A    SING  N  N  64  
365  O23    HO23    SING  N  N  65  
365  "C3'"  "H3'"   SING  N  N  66  
365  "C4'"  "H4'"   SING  N  N  67  
365  "C5'"  "H5'"   SING  N  N  68  
365  "C5'"  "H5'A"  SING  N  N  69  
365  O3P    HOP3    SING  N  N  70  
365  O2P    HOP2    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
365  InChI             InChI                 1.03   "InChI=1S/C21H27BN6O10P/c23-7-13-11-3-1-4-12(33-6-2-5-29)15(11)22(36-13)37-17-14(8-34-39(30,31)32)35-21(18(17)38-22)28-10-27-16-19(24)25-9-26-20(16)28/h1,3-4,9-10,13-14,17-18,21,29H,2,5-8,23H2,(H2,24,25,26)(H2,30,31,32)/q-1/p-2/t13-,14-,17-,18-,21-,22+/m1/s1"  
365  InChIKey          InChI                 1.03   SQCWYVPZBCHHDX-ZKDXOGESSA-L  
365  SMILES_CANONICAL  CACTVS                3.370  "NC[C@H]1O[B-]2(O[C@@H]3[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16"  
365  SMILES            CACTVS                3.370  "NC[CH]1O[B-]2(O[CH]3[CH](CO[P](O)(O)=O)O[CH]([CH]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16"  
365  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "[B-]12(c3c(cccc3OCCCO)[C@H](O1)CN)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O"  
365  SMILES            "OpenEye OEToolkits"  1.7.6  "[B-]12(c3c(cccc3OCCCO)C(O1)CN)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)(O)O"  
#
_pdbx_chem_comp_identifier.comp_id          365
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.7.6
_pdbx_chem_comp_identifier.identifier       "[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl 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
365  "Create component"  2013-01-21  EBI   
365  "Initial release"   2013-04-17  RCSB  
365  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     365
_pdbx_chem_comp_synonyms.name        "3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
