data_XDD
#

_chem_comp.id                                   XDD
_chem_comp.name                                 "N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine"
_chem_comp.type                                 peptide-like
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H19 N7 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-11
_chem_comp.pdbx_modified_date                   2020-12-18
_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                       333.346
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XDD
_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       7KZL
_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
XDD  C12   C1   C  0  1  N  N  N  -41.985  13.497  -12.851  -0.281   1.107   0.289  C12   XDD   1  
XDD  C14   C2   C  0  1  Y  N  N  -41.368  12.923  -10.476  -2.300   1.843  -1.035  C14   XDD   2  
XDD  C16   C3   C  0  1  Y  N  N  -39.733  13.228  -11.904  -2.646   0.211   0.408  C16   XDD   3  
XDD  C10   C4   C  0  1  N  N  N  -43.663  13.909  -16.723   3.372  -0.018   1.545  C10   XDD   4  
XDD  C11   C5   C  0  1  N  N  N  -42.487  12.231  -13.514   0.493   0.081  -0.498  C11   XDD   5  
XDD  C02   C6   C  0  1  N  N  N  -42.964  10.344  -16.118   2.601  -2.278  -0.608  C02   XDD   6  
XDD  C03   C7   C  0  1  N  N  N  -43.877  11.182  -15.235   2.598  -0.905  -1.229  C03   XDD   7  
XDD  C05   C8   C  0  1  N  N  S  -43.822  13.728  -15.075   2.527   0.857   0.596  C05   XDD   8  
XDD  C06   C9   C  0  1  N  N  S  -45.154  13.934  -14.883   3.508   1.799  -0.123  C06   XDD   9  
XDD  C08   C10  C  0  1  N  N  N  -45.477  15.204  -15.875   4.915   1.463   0.414  C08   XDD  10  
XDD  C09   C11  C  0  1  N  N  N  -44.521  14.969  -17.066   4.790   0.006   0.922  C09   XDD  11  
XDD  C17   C12  C  0  1  Y  N  N  -39.221  12.959  -10.643  -3.839   0.523  -0.266  C17   XDD  12  
XDD  C18   C13  C  0  1  Y  N  N  -37.824  12.957  -10.549  -4.996  -0.204   0.064  C18   XDD  13  
XDD  C21   C14  C  0  1  Y  N  N  -37.628  13.465  -12.783  -3.763  -1.405   1.601  C21   XDD  14  
XDD  N04   N1   N  0  1  N  N  N  -43.358  12.382  -14.636   1.834   0.013  -0.380  N04   XDD  15  
XDD  N07   N2   N  0  1  N  N  N  -45.471  14.260  -13.469   3.175   3.197   0.178  N07   XDD  16  
XDD  N13   N3   N  0  1  Y  N  N  -41.056  13.212  -11.755  -1.693   1.057  -0.100  N13   XDD  17  
XDD  N15   N4   N  0  1  Y  N  N  -40.236  12.759   -9.795  -3.559   1.530  -1.128  N15   XDD  18  
XDD  N19   N5   N  0  1  N  N  N  -37.174  12.696   -9.307  -6.200   0.058  -0.567  N19   XDD  19  
XDD  N20   N6   N  0  1  Y  N  N  -37.068  13.196  -11.606  -4.907  -1.148   0.995  N20   XDD  20  
XDD  N22   N7   N  0  1  Y  N  N  -38.946  13.481  -12.982  -2.653  -0.753   1.322  N22   XDD  21  
XDD  O01   O1   O  0  1  N  N  N  -43.380   9.307  -16.547   1.944  -2.495   0.382  O01   XDD  22  
XDD  O23   O2   O  0  1  N  N  N  -42.148  11.142  -13.143  -0.090  -0.683  -1.237  O23   XDD  23  
XDD  H121  H1   H  0  0  N  N  N  -41.469  14.111  -13.603  -0.191   0.892   1.354  H121  XDD  24  
XDD  H122  H2   H  0  0  N  N  N  -42.845  14.054  -12.451   0.118   2.100   0.083  H122  XDD  25  
XDD  H141  H3   H  0  0  N  N  N  -42.366  12.839  -10.072  -1.809   2.614  -1.610  H141  XDD  26  
XDD  H101  H4   H  0  0  N  N  N  -43.963  12.987  -17.242   3.388   0.411   2.547  H101  XDD  27  
XDD  H102  H5   H  0  0  N  N  N  -42.623  14.155  -16.985   2.983  -1.036   1.573  H102  XDD  28  
XDD  H032  H7   H  0  0  N  N  N  -44.740  11.476  -15.851   3.623  -0.545  -1.321  H032  XDD  29  
XDD  H031  H8   H  0  0  N  N  N  -44.216  10.533  -14.414   2.140  -0.953  -2.217  H031  XDD  30  
XDD  H051  H9   H  0  0  N  N  N  -43.214  14.508  -14.593   1.804   1.437   1.169  H051  XDD  31  
XDD  H061  H10  H  0  0  N  N  N  -45.757  13.077  -15.218   3.468   1.629  -1.199  H061  XDD  32  
XDD  H082  H11  H  0  0  N  N  N  -45.259  16.160  -15.376   5.653   1.526  -0.386  H082  XDD  33  
XDD  H081  H12  H  0  0  N  N  N  -46.527  15.192  -16.203   5.181   2.133   1.231  H081  XDD  34  
XDD  H092  H13  H  0  0  N  N  N  -43.934  15.879  -17.260   5.547  -0.206   1.677  H092  XDD  35  
XDD  H091  H14  H  0  0  N  N  N  -45.099  14.707  -17.964   4.860  -0.700   0.094  H091  XDD  36  
XDD  H211  H15  H  0  0  N  N  N  -36.981  13.682  -13.620  -3.735  -2.181   2.352  H211  XDD  37  
XDD  H2    H16  H  0  1  N  N  N  -45.265  13.471  -12.890   3.810   3.829  -0.287  H2    XDD  38  
XDD  H3    H17  H  0  1  N  N  N  -44.920  15.041  -13.176   2.218   3.402  -0.067  H3    XDD  39  
XDD  H192  H19  H  0  0  N  N  N  -36.183  12.736   -9.434  -6.252   0.750  -1.245  H192  XDD  40  
XDD  H191  H20  H  0  0  N  N  N  -37.452  13.382   -8.635  -6.992  -0.450  -0.331  H191  XDD  41  
XDD  O1    O3   O  0  1  N  Y  N  -41.737  11.010  -16.409   3.334  -3.260  -1.156  O1    XDD  42  
XDD  H1    H21  H  0  1  N  Y  N  -41.239  10.498  -17.036   3.304  -4.124  -0.722  H1    XDD  43  
#   #
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
XDD  C09  C10   SING  N  N   1  
XDD  C09  C08   SING  N  N   2  
XDD  C10  C05   SING  N  N   3  
XDD  O01  C02   DOUB  N  N   4  
XDD  C02  C03   SING  N  N   5  
XDD  C08  C06   SING  N  N   6  
XDD  C03  N04   SING  N  N   7  
XDD  C05  C06   SING  N  N   8  
XDD  C05  N04   SING  N  N   9  
XDD  C06  N07   SING  N  N  10  
XDD  N04  C11   SING  N  N  11  
XDD  C11  O23   DOUB  N  N  12  
XDD  C11  C12   SING  N  N  13  
XDD  N22  C21   DOUB  Y  N  14  
XDD  N22  C16   SING  Y  N  15  
XDD  C12  N13   SING  N  N  16  
XDD  C21  N20   SING  Y  N  17  
XDD  C16  N13   SING  Y  N  18  
XDD  C16  C17   DOUB  Y  N  19  
XDD  N13  C14   SING  Y  N  20  
XDD  N20  C18   DOUB  Y  N  21  
XDD  C17  C18   SING  Y  N  22  
XDD  C17  N15   SING  Y  N  23  
XDD  C18  N19   SING  N  N  24  
XDD  C14  N15   DOUB  Y  N  25  
XDD  C12  H121  SING  N  N  26  
XDD  C12  H122  SING  N  N  27  
XDD  C14  H141  SING  N  N  28  
XDD  C10  H101  SING  N  N  29  
XDD  C10  H102  SING  N  N  30  
XDD  C03  H032  SING  N  N  31  
XDD  C03  H031  SING  N  N  32  
XDD  C05  H051  SING  N  N  33  
XDD  C06  H061  SING  N  N  34  
XDD  C08  H082  SING  N  N  35  
XDD  C08  H081  SING  N  N  36  
XDD  C09  H092  SING  N  N  37  
XDD  C09  H091  SING  N  N  38  
XDD  C21  H211  SING  N  N  39  
XDD  N07  H2    SING  N  N  40  
XDD  N07  H3    SING  N  N  41  
XDD  N19  H192  SING  N  N  42  
XDD  N19  H191  SING  N  N  43  
XDD  C02  O1    SING  N  N  44  
XDD  O1   H1    SING  N  N  45  
#   #
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
XDD  SMILES            ACDLabs               12.01  "C(n1cnc2c1ncnc2N)C(=O)N(CC(O)=O)C3CCCC3N"  
XDD  InChI             InChI                 1.03   "InChI=1S/C14H19N7O3/c15-8-2-1-3-9(8)21(5-11(23)24)10(22)4-20-7-19-12-13(16)17-6-18-14(12)20/h6-9H,1-5,15H2,(H,23,24)(H2,16,17,18)/t8-,9-/m0/s1"  
XDD  InChIKey          InChI                 1.03   ZTNYOEGLXUSDRB-IUCAKERBSA-N  
XDD  SMILES_CANONICAL  CACTVS                3.385  "N[C@H]1CCC[C@@H]1N(CC(O)=O)C(=O)Cn2cnc3c(N)ncnc23"  
XDD  SMILES            CACTVS                3.385  "N[CH]1CCC[CH]1N(CC(O)=O)C(=O)Cn2cnc3c(N)ncnc23"  
XDD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)CC(=O)N(CC(=O)O)[C@H]3CCC[C@@H]3N)N"  
XDD  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)CC(=O)N(CC(=O)O)C3CCCC3N)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
XDD  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine"  
XDD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "2-[2-(6-aminopurin-9-yl)ethanoyl-[(1~{S},2~{S})-2-azanylcyclopentyl]amino]ethanoic 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
XDD  "Create component"  2020-12-11  RCSB  
XDD  "Initial release"   2020-12-23  RCSB  
##
