data_XDJ
# 
_chem_comp.id                                    XDJ 
_chem_comp.name                                  "N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine" 
_chem_comp.type                                  peptide-like 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H19 N7 O4" 
_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                    2024-09-27 
_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                        349.345 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XDJ 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
XDJ C    C02  C 0 1 N N N Y N Y -33.963 2.968 -15.770 2.694  -2.169 -0.965 C02  XDJ 1  
XDJ C03  C03  C 0 1 N N N Y N N -35.131 3.819 -16.132 2.777  -0.716 -1.360 C03  XDJ 2  
XDJ C05  C05  C 0 1 N N S Y N N -34.894 6.371 -16.355 2.710  0.732  0.723  C05  XDJ 3  
XDJ CA   C06  C 0 1 N N S Y N N -35.724 6.659 -17.382 3.755  1.734  0.200  C06  XDJ 4  
XDJ C08  C08  C 0 1 N N N N N N -34.820 7.562 -18.382 5.126  1.250  0.717  C08  XDJ 5  
XDJ C09  C09  C 0 1 N N N N N N -33.536 7.090 -18.341 4.922  -0.265 0.973  C09  XDJ 6  
XDJ C10  C10  C 0 1 N N N N N N -33.446 6.142 -17.070 3.481  -0.326 1.539  C10  XDJ 7  
XDJ C11  C11  C 0 1 N N N N N N -35.686 5.233 -14.196 0.692  0.252  -0.555 C11  XDJ 8  
XDJ C12  C12  C 0 1 N N N N N N -35.845 6.639 -13.630 -0.068 1.178  0.360  C12  XDJ 9  
XDJ C14  C14  C 0 1 Y N N N N N -37.522 6.537 -11.771 -1.985 2.231  -0.900 C14  XDJ 10 
XDJ C16  C16  C 0 1 Y N N N N N -35.438 6.658 -11.230 -2.473 0.410  0.242  C16  XDJ 11 
XDJ C17  C17  C 0 1 Y N N N N N -36.192 6.630 -10.104 -3.615 0.888  -0.411 C17  XDJ 12 
XDJ C18  C18  C 0 1 N N N N N N -35.490 6.692 -8.797  -4.831 0.184  -0.252 C18  XDJ 13 
XDJ C20  C20  C 0 1 N N N N N N -33.394 6.757 -10.065 -3.690 -1.338 1.136  C20  XDJ 14 
XDJ N04  N04  N 0 1 N N N Y N N -35.195 5.131 -15.543 2.021  0.094  -0.402 N04  XDJ 15 
XDJ N    N07  N 0 1 N N N Y Y N -36.937 7.443 -17.055 3.468  3.077  0.719  N07  XDJ 16 
XDJ N13  N13  N 0 1 Y N N N N N -36.284 6.614 -12.244 -1.460 1.271  -0.084 N13  XDJ 17 
XDJ N15  N15  N 0 1 Y N N N N N -37.479 6.545 -10.436 -3.253 2.005  -1.088 N15  XDJ 18 
XDJ N19  N19  N 0 1 N N N N N N -34.113 6.756 -8.883  -4.835 -0.922 0.525  N19  XDJ 19 
XDJ N21  N21  N 0 1 N N N N N N -32.040 6.797 -10.002 -3.724 -2.464 1.919  N21  XDJ 20 
XDJ N22  N22  N 0 1 N N N N N N -34.027 6.732 -11.302 -2.552 -0.696 0.991  N22  XDJ 21 
XDJ O    O01  O 0 1 N N N Y N Y -33.875 1.951 -16.400 1.980  -2.506 -0.051 O01  XDJ 22 
XDJ O23  O23  O 0 1 N N N N N N -36.020 6.688 -7.712  -5.850 0.565  -0.802 O23  XDJ 23 
XDJ O24  O24  O 0 1 N N N N N N -35.949 4.260 -13.574 0.106  -0.350 -1.430 O24  XDJ 24 
XDJ H031 H031 H 0 0 N N N Y N N -35.122 3.947 -17.225 3.820  -0.400 -1.360 H031 XDJ 25 
XDJ H032 H032 H 0 0 N N N Y N N -36.041 3.277 -15.834 2.358  -0.586 -2.357 H032 XDJ 26 
XDJ H051 H051 H 0 0 N N N Y N N -34.793 7.228 -15.672 1.989  1.244  1.360  H051 XDJ 27 
XDJ HA   H061 H 0 0 N N N Y N N -36.015 5.749 -17.927 3.749  1.745  -0.889 H061 XDJ 28 
XDJ H081 H081 H 0 0 N N N N N N -34.841 8.613 -18.057 5.896  1.409  -0.037 H081 XDJ 29 
XDJ H082 H082 H 0 0 N N N N N N -35.212 7.488 -19.407 5.386  1.761  1.644  H082 XDJ 30 
XDJ H092 H092 H 0 0 N N N N N N -33.310 6.522 -19.256 4.996  -0.826 0.041  H092 XDJ 31 
XDJ H091 H091 H 0 0 N N N N N N -32.827 7.925 -18.243 5.641  -0.633 1.705  H091 XDJ 32 
XDJ H102 H102 H 0 0 N N N N N N -33.311 5.091 -17.367 3.476  -0.068 2.598  H102 XDJ 33 
XDJ H101 H101 H 0 0 N N N N N N -32.623 6.444 -16.406 3.051  -1.315 1.384  H101 XDJ 34 
XDJ H122 H122 H 0 0 N N N N N N -34.877 7.158 -13.688 -0.036 0.789  1.378  H122 XDJ 35 
XDJ H121 H121 H 0 0 N N N N N N -36.589 7.183 -14.230 0.388  2.168  0.335  H121 XDJ 36 
XDJ H141 H141 H 0 0 N N N N N N -38.419 6.477 -12.369 -1.432 3.057  -1.322 H141 XDJ 37 
XDJ H    H071 H 0 0 N N N Y Y N -37.520 6.914 -16.438 4.145  3.747  0.386  H071 XDJ 38 
XDJ H2   H3   H 0 1 N Y N Y Y N -36.671 8.299 -16.611 2.530  3.364  0.482  H3   XDJ 39 
XDJ H191 H191 H 0 0 N N N N N N -33.598 6.805 -8.028  -5.658 -1.418 0.654  H191 XDJ 40 
XDJ H211 H211 H 0 0 N N N N N N -31.500 6.808 -10.844 -4.555 -2.952 2.032  H211 XDJ 41 
XDJ H212 H212 H 0 0 N N N N N N -31.581 6.815 -9.114  -2.917 -2.773 2.360  H212 XDJ 42 
XDJ OXT  O1   O 0 1 N Y N Y N Y -32.966 3.539 -14.927 3.408  -3.088 -1.633 O1   XDJ 43 
XDJ HXT  H1   H 0 1 N Y N Y N Y -32.193 2.986 -14.930 3.322  -4.006 -1.344 H1   XDJ 44 
# 
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 
XDJ C08 C09  SING N N 1  
XDJ C08 CA   SING N N 2  
XDJ C09 C10  SING N N 3  
XDJ CA  N    SING N N 4  
XDJ CA  C05  SING N N 5  
XDJ C10 C05  SING N N 6  
XDJ O   C    DOUB N N 7  
XDJ C05 N04  SING N N 8  
XDJ C03 C    SING N N 9  
XDJ C03 N04  SING N N 10 
XDJ N04 C11  SING N N 11 
XDJ C11 C12  SING N N 12 
XDJ C11 O24  DOUB N N 13 
XDJ C12 N13  SING N N 14 
XDJ N13 C14  SING Y N 15 
XDJ N13 C16  SING Y N 16 
XDJ C14 N15  DOUB Y N 17 
XDJ N22 C16  SING N N 18 
XDJ N22 C20  DOUB N N 19 
XDJ C16 C17  DOUB Y N 20 
XDJ N15 C17  SING Y N 21 
XDJ C17 C18  SING N N 22 
XDJ C20 N21  SING N N 23 
XDJ C20 N19  SING N N 24 
XDJ N19 C18  SING N N 25 
XDJ C18 O23  DOUB N N 26 
XDJ C03 H031 SING N N 27 
XDJ C03 H032 SING N N 28 
XDJ C05 H051 SING N N 29 
XDJ CA  HA   SING N N 30 
XDJ C08 H081 SING N N 31 
XDJ C08 H082 SING N N 32 
XDJ C09 H092 SING N N 33 
XDJ C09 H091 SING N N 34 
XDJ C10 H102 SING N N 35 
XDJ C10 H101 SING N N 36 
XDJ C12 H122 SING N N 37 
XDJ C12 H121 SING N N 38 
XDJ C14 H141 SING N N 39 
XDJ N   H    SING N N 40 
XDJ N   H2   SING N N 41 
XDJ N19 H191 SING N N 42 
XDJ N21 H211 SING N N 43 
XDJ N21 H212 SING N N 44 
XDJ C   OXT  SING N N 45 
XDJ OXT HXT  SING N N 46 
# 
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 
XDJ SMILES           ACDLabs              12.01 "C(O)(CN(C1C(N)CCC1)C(Cn2cnc3c2N=C(N)NC3=O)=O)=O"                                                                                                      
XDJ InChI            InChI                1.03  "InChI=1S/C14H19N7O4/c15-7-2-1-3-8(7)21(5-10(23)24)9(22)4-20-6-17-11-12(20)18-14(16)19-13(11)25/h6-8H,1-5,15H2,(H,23,24)(H3,16,18,19,25)/t7-,8-/m0/s1" 
XDJ InChIKey         InChI                1.03  WUJTVJFBNNNLRX-YUMQZZPRSA-N                                                                                                                            
XDJ SMILES_CANONICAL CACTVS               3.385 "N[C@H]1CCC[C@@H]1N(CC(O)=O)C(=O)Cn2cnc3C(=O)NC(=Nc23)N"                                                                                               
XDJ SMILES           CACTVS               3.385 "N[CH]1CCC[CH]1N(CC(O)=O)C(=O)Cn2cnc3C(=O)NC(=Nc23)N"                                                                                                  
XDJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1CC(=O)N(CC(=O)O)[C@H]3CCC[C@@H]3N)N=C(NC2=O)N"                                                                                               
XDJ SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1CC(=O)N(CC(=O)O)C3CCCC3N)N=C(NC2=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 
XDJ "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine"                         
XDJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[[(1~{S},2~{S})-2-azanylcyclopentyl]-[2-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)ethanoyl]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 
XDJ "Create component" 2020-12-11 RCSB 
XDJ "Initial release"  2020-12-23 RCSB 
XDJ "Modify backbone"  2023-11-03 PDBE 
XDJ "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XDJ 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain and backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
