data_Q2M
#

_chem_comp.id                                   Q2M
_chem_comp.name                                 "5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(thiophen-2-yl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H32 N8 O5 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-09-11
_chem_comp.pdbx_modified_date                   2020-06-26
_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                       532.616
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Q2M
_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       6U9M
_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
Q2M  C1   C1   C  0  1  Y  N  N  16.411  -23.264   8.367   5.891  -3.787  -0.516  C1   Q2M   1  
Q2M  C2   C2   C  0  1  Y  N  N  17.529  -21.512   9.317   4.507  -1.953  -0.465  C2   Q2M   2  
Q2M  C3   C3   C  0  1  Y  N  N  17.718  -20.905   8.045   5.205  -1.409  -1.556  C3   Q2M   3  
Q2M  C4   C4   C  0  1  Y  N  N  18.614  -19.543   9.472   3.650   0.002  -1.017  C4   Q2M   4  
Q2M  C5   C5   C  0  1  N  N  R  18.328  -20.882  11.659   2.534  -1.175   0.916  C5   Q2M   5  
Q2M  C6   C6   C  0  1  N  N  R  19.472  -21.931  11.881   3.109  -0.664   2.262  C6   Q2M   6  
Q2M  C7   C7   C  0  1  N  N  S  20.680  -20.993  12.002   1.825  -0.283   3.039  C7   Q2M   7  
Q2M  C8   C8   C  0  1  N  N  R  20.035  -19.856  12.815   0.761  -0.094   1.941  C8   Q2M   8  
Q2M  O1   O1   O  0  1  N  N  N  21.768  -21.562  12.655   1.446  -1.338   3.927  O1   Q2M   9  
Q2M  N1   N1   N  0  1  Y  N  N  16.537  -22.805   7.073   6.581  -3.314  -1.539  N1   Q2M  10  
Q2M  N2   N2   N  0  1  Y  N  N  16.870  -22.713   9.531   4.878  -3.136   0.014  N2   Q2M  11  
Q2M  N    N3   N  0  1  N  N  N  17.385  -21.137   5.648   7.008  -1.655  -3.159  N    Q2M  12  
Q2M  C    C9   C  0  1  Y  N  N  17.209  -21.614   6.904   6.280  -2.142  -2.088  C    Q2M  13  
Q2M  O    O2   O  0  1  N  N  N  19.150  -22.568  13.072   3.825  -1.700   2.937  O    Q2M  14  
Q2M  O3   O3   O  0  1  N  N  N  17.400  -15.575  15.910   0.754   6.007  -1.982  O3   Q2M  15  
Q2M  C22  C10  C  0  1  N  N  N  16.734  -15.917  14.939   0.828   5.702  -0.816  C22  Q2M  16  
Q2M  O2   O4   O  0  1  N  N  N  15.390  -15.827  15.011   1.951   5.956  -0.125  O2   Q2M  17  
Q2M  C21  C11  C  0  1  N  N  S  17.274  -16.489  13.599  -0.340   5.038  -0.135  C21  Q2M  18  
Q2M  N7   N4   N  0  1  N  N  N  16.236  -16.565  12.551  -1.554   5.240  -0.938  N7   Q2M  19  
Q2M  C20  C12  C  0  1  N  N  N  18.427  -15.545  13.123  -0.065   3.539   0.003  C20  Q2M  20  
Q2M  C19  C13  C  0  1  N  N  N  19.614  -16.328  12.483  -1.203   2.881   0.786  C19  Q2M  21  
Q2M  N5   N5   N  0  1  N  N  N  20.116  -17.438  13.410  -0.885   1.466   1.016  N5   Q2M  22  
Q2M  C10  C14  C  0  1  N  N  N  20.831  -16.983  14.663  -2.082   0.716   1.421  C10  Q2M  23  
Q2M  C11  C15  C  0  1  N  N  N  20.747  -18.113  15.743  -3.079   0.681   0.261  C11  Q2M  24  
Q2M  C18  C16  C  0  1  N  N  N  20.906  -17.763  17.250  -2.868  -0.502  -0.701  C18  Q2M  25  
Q2M  N6   N6   N  0  1  N  N  N  19.671  -18.586  17.557  -4.341  -0.633  -0.705  N6   Q2M  26  
Q2M  C13  C17  C  0  1  N  N  N  18.688  -17.998  18.516  -4.745  -2.043  -0.620  C13  Q2M  27  
Q2M  C14  C18  C  0  1  Y  N  N  17.437  -18.821  18.522  -6.226  -2.158  -0.872  C14  Q2M  28  
Q2M  S    S1   S  0  1  Y  N  N  17.492  -20.548  18.454  -7.475  -2.071   0.364  S    Q2M  29  
Q2M  C17  C19  C  0  1  Y  N  N  15.785  -20.664  18.448  -8.730  -2.294  -0.847  C17  Q2M  30  
Q2M  C16  C20  C  0  1  Y  N  N  15.188  -19.448  18.498  -8.173  -2.416  -2.053  C16  Q2M  31  
Q2M  C15  C21  C  0  1  Y  N  N  16.153  -18.367  18.545  -6.791  -2.336  -2.067  C15  Q2M  32  
Q2M  C12  C22  C  0  1  N  N  N  19.291  -18.561  16.109  -4.423   0.023   0.619  C12  Q2M  33  
Q2M  C9   C23  C  0  1  N  N  N  20.841  -18.541  12.648   0.187   1.322   2.010  C9   Q2M  34  
Q2M  O4   O5   O  0  1  N  N  N  18.704  -19.710  12.332   1.411  -0.300   0.676  O4   Q2M  35  
Q2M  N4   N7   N  0  1  Y  N  N  18.124  -20.647  10.227   3.528  -1.045  -0.152  N4   Q2M  36  
Q2M  N3   N8   N  0  1  Y  N  N  18.388  -19.673   8.167   4.633  -0.215  -1.841  N3   Q2M  37  
Q2M  H7   H1   H  0  1  N  N  N  15.872  -24.193   8.477   6.166  -4.747  -0.103  H7   Q2M  38  
Q2M  H8   H2   H  0  1  N  N  N  19.115  -18.693   9.911   3.018   0.878  -1.022  H8   Q2M  39  
Q2M  H    H3   H  0  1  N  N  N  17.404  -21.290  12.095   2.202  -2.209   1.009  H    Q2M  40  
Q2M  H1   H4   H  0  1  N  N  N  19.566  -22.608  11.019   3.743   0.209   2.108  H1   Q2M  41  
Q2M  H2   H5   H  0  1  N  N  N  20.956  -20.619  11.005   1.974   0.644   3.592  H2   Q2M  42  
Q2M  H3   H6   H  0  1  N  N  N  20.031  -20.136  13.879  -0.039  -0.824   2.070  H3   Q2M  43  
Q2M  H10  H7   H  0  1  N  N  N  22.478  -20.932  12.696   2.107  -1.539   4.603  H10  Q2M  44  
Q2M  H5   H8   H  0  1  N  N  N  16.971  -21.767   4.991   7.748  -2.170  -3.517  H5   Q2M  45  
Q2M  H6   H9   H  0  1  N  N  N  16.951  -20.240   5.568   6.779  -0.798  -3.552  H6   Q2M  46  
Q2M  H9   H10  H  0  1  N  N  N  19.809  -23.224  13.269   4.204  -1.429   3.784  H9   Q2M  47  
Q2M  H29  H11  H  0  1  N  N  N  15.140  -15.488  15.863   2.674   6.384  -0.605  H29  Q2M  48  
Q2M  H4   H12  H  0  1  N  N  N  17.692  -17.490  13.783  -0.481   5.474   0.854  H4   Q2M  49  
Q2M  H15  H13  H  0  1  N  N  N  15.499  -17.168  12.855  -1.449   4.844  -1.860  H15  Q2M  50  
Q2M  H31  H14  H  0  1  N  N  N  15.869  -15.651  12.379  -2.364   4.859  -0.471  H31  Q2M  51  
Q2M  H27  H16  H  0  1  N  N  N  18.803  -14.982  13.990   0.002   3.089  -0.987  H27  Q2M  52  
Q2M  H28  H17  H  0  1  N  N  N  18.024  -14.844  12.377   0.875   3.390   0.535  H28  Q2M  53  
Q2M  H26  H18  H  0  1  N  N  N  19.278  -16.777  11.537  -1.325   3.387   1.744  H26  Q2M  54  
Q2M  H25  H19  H  0  1  N  N  N  20.439  -15.628  12.284  -2.128   2.957   0.215  H25  Q2M  55  
Q2M  H13  H21  H  0  1  N  N  N  21.886  -16.775  14.430  -1.800  -0.302   1.689  H13  Q2M  56  
Q2M  H14  H22  H  0  1  N  N  N  20.353  -16.070  15.048  -2.542   1.204   2.281  H14  Q2M  57  
Q2M  H33  H23  H  0  1  N  N  N  21.370  -18.976  15.465  -3.181   1.644  -0.240  H33  Q2M  58  
Q2M  H24  H24  H  0  1  N  N  N  21.830  -18.147  17.707  -2.450  -0.214  -1.666  H24  Q2M  59  
Q2M  H23  H25  H  0  1  N  N  N  20.802  -16.692  17.478  -2.352  -1.349  -0.249  H23  Q2M  60  
Q2M  H18  H27  H  0  1  N  N  N  19.124  -17.987  19.526  -4.203  -2.622  -1.368  H18  Q2M  61  
Q2M  H19  H28  H  0  1  N  N  N  18.448  -16.969  18.209  -4.514  -2.427   0.374  H19  Q2M  62  
Q2M  H22  H29  H  0  1  N  N  N  15.245  -21.599  18.409  -9.791  -2.328  -0.646  H22  Q2M  63  
Q2M  H21  H30  H  0  1  N  N  N  14.118  -19.301  18.502  -8.755  -2.562  -2.951  H21  Q2M  64  
Q2M  H20  H31  H  0  1  N  N  N  15.885  -17.322  18.593  -6.214  -2.414  -2.977  H20  Q2M  65  
Q2M  H16  H32  H  0  1  N  N  N  18.516  -17.821  15.860  -4.363  -0.671   1.457  H16  Q2M  66  
Q2M  H17  H33  H  0  1  N  N  N  19.006  -19.542  15.701  -5.248   0.730   0.709  H17  Q2M  67  
Q2M  H11  H34  H  0  1  N  N  N  21.854  -18.671  13.056  -0.215   1.503   3.007  H11  Q2M  68  
Q2M  H12  H35  H  0  1  N  N  N  20.906  -18.277  11.582   0.976   2.044   1.800  H12  Q2M  69  
#   #
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
Q2M  N    C    SING  N  N   1  
Q2M  C    N1   DOUB  Y  N   2  
Q2M  C    C3   SING  Y  N   3  
Q2M  N1   C1   SING  Y  N   4  
Q2M  C3   N3   SING  Y  N   5  
Q2M  C3   C2   DOUB  Y  N   6  
Q2M  N3   C4   DOUB  Y  N   7  
Q2M  C1   N2   DOUB  Y  N   8  
Q2M  C2   N2   SING  Y  N   9  
Q2M  C2   N4   SING  Y  N  10  
Q2M  C4   N4   SING  Y  N  11  
Q2M  N4   C5   SING  N  N  12  
Q2M  C5   C6   SING  N  N  13  
Q2M  C5   O4   SING  N  N  14  
Q2M  C6   C7   SING  N  N  15  
Q2M  C6   O    SING  N  N  16  
Q2M  C7   O1   SING  N  N  17  
Q2M  C7   C8   SING  N  N  18  
Q2M  O4   C8   SING  N  N  19  
Q2M  C19  C20  SING  N  N  20  
Q2M  C19  N5   SING  N  N  21  
Q2M  N7   C21  SING  N  N  22  
Q2M  C9   C8   SING  N  N  23  
Q2M  C9   N5   SING  N  N  24  
Q2M  C20  C21  SING  N  N  25  
Q2M  N5   C10  SING  N  N  26  
Q2M  C21  C22  SING  N  N  27  
Q2M  C10  C11  SING  N  N  28  
Q2M  C22  O2   SING  N  N  29  
Q2M  C22  O3   DOUB  N  N  30  
Q2M  C11  C12  SING  N  N  31  
Q2M  C11  C18  SING  N  N  32  
Q2M  C12  N6   SING  N  N  33  
Q2M  C18  N6   SING  N  N  34  
Q2M  N6   C13  SING  N  N  35  
Q2M  C17  S    SING  Y  N  36  
Q2M  C17  C16  DOUB  Y  N  37  
Q2M  S    C14  SING  Y  N  38  
Q2M  C16  C15  SING  Y  N  39  
Q2M  C13  C14  SING  N  N  40  
Q2M  C14  C15  DOUB  Y  N  41  
Q2M  C1   H7   SING  N  N  42  
Q2M  C4   H8   SING  N  N  43  
Q2M  C5   H    SING  N  N  44  
Q2M  C6   H1   SING  N  N  45  
Q2M  C7   H2   SING  N  N  46  
Q2M  C8   H3   SING  N  N  47  
Q2M  O1   H10  SING  N  N  48  
Q2M  N    H5   SING  N  N  49  
Q2M  N    H6   SING  N  N  50  
Q2M  O    H9   SING  N  N  51  
Q2M  O2   H29  SING  N  N  52  
Q2M  C21  H4   SING  N  N  53  
Q2M  N7   H15  SING  N  N  54  
Q2M  N7   H31  SING  N  N  55  
Q2M  C20  H27  SING  N  N  56  
Q2M  C20  H28  SING  N  N  57  
Q2M  C19  H26  SING  N  N  58  
Q2M  C19  H25  SING  N  N  59  
Q2M  C10  H13  SING  N  N  60  
Q2M  C10  H14  SING  N  N  61  
Q2M  C11  H33  SING  N  N  62  
Q2M  C18  H24  SING  N  N  63  
Q2M  C18  H23  SING  N  N  64  
Q2M  C13  H18  SING  N  N  65  
Q2M  C13  H19  SING  N  N  66  
Q2M  C17  H22  SING  N  N  67  
Q2M  C16  H21  SING  N  N  68  
Q2M  C15  H20  SING  N  N  69  
Q2M  C12  H16  SING  N  N  70  
Q2M  C12  H17  SING  N  N  71  
Q2M  C9   H11  SING  N  N  72  
Q2M  C9   H12  SING  N  N  73  
#   #
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
Q2M  SMILES            ACDLabs               12.01  "c2nc1n(cnc1c(n2)N)C5C(C(O)C(CN(CCC(C(=O)O)N)CC3CN(C3)Cc4cccs4)O5)O"  
Q2M  InChI             InChI                 1.03   "InChI=1S/C23H32N8O5S/c24-15(23(34)35)3-4-29(6-13-7-30(8-13)9-14-2-1-5-37-14)10-16-18(32)19(33)22(36-16)31-12-28-17-20(25)26-11-27-21(17)31/h1-2,5,11-13,15-16,18-19,22,32-33H,3-4,6-10,24H2,(H,34,35)(H2,25,26,27)/t15-,16+,18+,19+,22+/m0/s1"  
Q2M  InChIKey          InChI                 1.03   KJOQVBZBXKPYJX-XVZIYINBSA-N  
Q2M  SMILES_CANONICAL  CACTVS                3.385  "N[C@@H](CCN(CC1CN(C1)Cc2sccc2)C[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C(O)=O"  
Q2M  SMILES            CACTVS                3.385  "N[CH](CCN(CC1CN(C1)Cc2sccc2)C[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C(O)=O"  
Q2M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(sc1)CN2CC(C2)CN(CC[C@@H](C(=O)O)N)C[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O"  
Q2M  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(sc1)CN2CC(C2)CN(CCC(C(=O)O)N)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O"  
#   #
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
Q2M  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(thiophen-2-yl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine"  
Q2M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[[1-(thiophen-2-ylmethyl)azetidin-3-yl]methyl]amino]-2-azanyl-butanoic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Q2M  "Create component"  2019-09-11  RCSB  
Q2M  "Initial release"   2020-07-01  RCSB  
##
