data_XDY
# 
_chem_comp.id                                    XDY 
_chem_comp.name                                  "N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine" 
_chem_comp.type                                  peptide-like 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H20 N4 O5" 
_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                    2023-11-03 
_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                        324.332 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XDY 
_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.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 
XDY C    C02  C 0 1 N N N Y N Y -38.208 6.784  -17.091 -2.190 2.222  -0.568 C02  XDY 1  
XDY C03  C03  C 0 1 N N N Y N N -39.263 7.612  -17.055 -2.133 0.817  -1.111 C03  XDY 2  
XDY C05  C05  C 0 1 N N S Y N N -39.451 10.164 -16.961 -2.512 -0.837 0.775  C05  XDY 3  
XDY CA   C06  C 0 1 N N S Y N N -40.881 10.402 -17.452 -3.378 -1.781 -0.076 C06  XDY 4  
XDY C08  C08  C 0 1 N N N N N N -40.792 11.306 -18.692 -4.845 -1.359 0.151  C08  XDY 5  
XDY C09  C09  C 0 1 N N N N N N -39.280 11.293 -19.113 -4.748 0.121  0.600  C09  XDY 6  
XDY C10  C10  C 0 1 N N N N N N -38.556 10.239 -18.202 -3.481 0.126  1.492  C10  XDY 7  
XDY C11  C11  C 0 1 N N N N N N -39.046 8.827  -14.887 -0.265 -0.213 0.067  C11  XDY 8  
XDY C12  C12  C 0 1 N N N N N N -39.040 10.101 -14.106 0.674  0.476  -0.889 C12  XDY 9  
XDY C14  C14  C 0 1 N N N N N N -37.364 9.902  -12.337 2.674  -0.898 -1.035 C14  XDY 10 
XDY C16  C16  C 0 1 N N N N N N -38.083 9.592  -9.994  4.625  -0.412 0.156  C16  XDY 11 
XDY C17  C17  C 0 1 N N N N N N -39.495 9.549  -10.439 3.989  0.724  0.712  C17  XDY 12 
XDY C18  C18  C 0 1 N N N N N N -39.776 9.683  -11.747 2.713  0.998  0.366  C18  XDY 13 
XDY C19  C19  C 0 1 N N N N N N -40.579 9.369  -9.411  4.727  1.616  1.678  C19  XDY 14 
XDY N04  N04  N 0 1 N N N Y N N -39.253 8.873  -16.285 -1.598 -0.082 -0.085 N04  XDY 15 
XDY N    N07  N 0 1 N N N Y Y N -41.737 11.010 -16.409 -3.182 -3.171 0.356  N07  XDY 16 
XDY N13  N13  N 0 1 N N N N N N -38.721 9.909  -12.708 2.058  0.179  -0.513 N13  XDY 17 
XDY N15  N15  N 0 1 N N N N N N -37.106 9.762  -10.975 3.945  -1.194 -0.707 N15  XDY 18 
XDY O    O01  O 0 1 N N N Y N Y -38.368 5.652  -17.483 -1.722 2.469  0.518  O01  XDY 19 
XDY O20  O20  O 0 1 N N N N N N -37.761 9.486  -8.837  5.775  -0.679 0.453  O20  XDY 20 
XDY O21  O21  O 0 1 N N N N N N -36.475 10.039 -13.115 2.072  -1.615 -1.810 O21  XDY 21 
XDY O22  O22  O 0 1 N N N N N N -38.889 7.801  -14.313 0.178  -0.887 0.973  O22  XDY 22 
XDY H032 H032 H 0 0 N N N Y N N -39.468 7.892  -18.099 -3.136 0.494  -1.390 H032 XDY 23 
XDY H031 H031 H 0 0 N N N Y N N -40.103 7.020  -16.663 -1.486 0.793  -1.988 H031 XDY 24 
XDY H051 H051 H 0 0 N N N Y N N -39.174 10.981 -16.278 -1.945 -1.411 1.509  H051 XDY 25 
XDY HA   H061 H 0 0 N N N Y N N -41.312 9.436  -17.755 -3.119 -1.678 -1.130 H061 XDY 26 
XDY H081 H081 H 0 0 N N N N N N -41.114 12.329 -18.446 -5.413 -1.440 -0.775 H081 XDY 27 
XDY H082 H082 H 0 0 N N N N N N -41.420 10.909 -19.503 -5.300 -1.967 0.932  H082 XDY 28 
XDY H092 H092 H 0 0 N N N N N N -39.185 11.006 -20.171 -4.619 0.778  -0.260 H092 XDY 29 
XDY H091 H091 H 0 0 N N N N N N -38.838 12.289 -18.962 -5.628 0.407  1.177  H091 XDY 30 
XDY H101 H101 H 0 0 N N N N N N -38.496 9.262  -18.703 -3.716 -0.241 2.491  H101 XDY 31 
XDY H102 H102 H 0 0 N N N N N N -37.544 10.578 -17.937 -3.055 1.128  1.543  H102 XDY 32 
XDY H121 H121 H 0 0 N N N N N N -38.292 10.778 -14.546 0.488  0.120  -1.902 H121 XDY 33 
XDY H122 H122 H 0 0 N N N N N N -40.037 10.560 -14.178 0.509  1.553  -0.846 H122 XDY 34 
XDY H181 H181 H 0 0 N N N N N N -40.801 9.621  -12.083 2.212  1.861  0.780  H181 XDY 35 
XDY H191 H191 H 0 0 N N N N N N -40.127 9.280  -8.412  5.735  1.232  1.829  H191 XDY 36 
XDY H192 H192 H 0 0 N N N N N N -41.253 10.238 -9.432  4.780  2.626  1.271  H192 XDY 37 
XDY H193 H193 H 0 0 N N N N N N -41.151 8.457  -9.637  4.198  1.635  2.631  H193 XDY 38 
XDY H    H071 H 0 0 N N N Y Y N -41.778 10.403 -15.615 -3.745 -3.803 -0.194 H071 XDY 39 
XDY H2   H2   H 0 1 N Y N Y Y N -41.353 11.892 -16.135 -2.207 -3.428 0.317  H2   XDY 40 
XDY H151 H151 H 0 0 N N N N N N -36.151 9.785  -10.679 4.374  -1.974 -1.092 H151 XDY 41 
XDY OXT  O1   O 0 1 N Y N Y N Y -36.937 7.443  -17.055 -2.756 3.199  -1.293 O1   XDY 42 
XDY HXT  H1   H 0 1 N Y N Y N Y -36.266 6.855  -17.382 -2.769 4.084  -0.903 H1   XDY 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 
XDY C09 C08  SING N N 1  
XDY C09 C10  SING N N 2  
XDY C08 CA   SING N N 3  
XDY C10 C05  SING N N 4  
XDY O   C    DOUB N N 5  
XDY CA  C05  SING N N 6  
XDY CA  N    SING N N 7  
XDY C   C03  SING N N 8  
XDY C03 N04  SING N N 9  
XDY C05 N04  SING N N 10 
XDY N04 C11  SING N N 11 
XDY C11 O22  DOUB N N 12 
XDY C11 C12  SING N N 13 
XDY C12 N13  SING N N 14 
XDY O21 C14  DOUB N N 15 
XDY N13 C14  SING N N 16 
XDY N13 C18  SING N N 17 
XDY C14 N15  SING N N 18 
XDY C18 C17  DOUB N N 19 
XDY N15 C16  SING N N 20 
XDY C17 C16  SING N N 21 
XDY C17 C19  SING N N 22 
XDY C16 O20  DOUB N N 23 
XDY C03 H032 SING N N 24 
XDY C03 H031 SING N N 25 
XDY C05 H051 SING N N 26 
XDY CA  HA   SING N N 27 
XDY C08 H081 SING N N 28 
XDY C08 H082 SING N N 29 
XDY C09 H092 SING N N 30 
XDY C09 H091 SING N N 31 
XDY C10 H101 SING N N 32 
XDY C10 H102 SING N N 33 
XDY C12 H121 SING N N 34 
XDY C12 H122 SING N N 35 
XDY C18 H181 SING N N 36 
XDY C19 H191 SING N N 37 
XDY C19 H192 SING N N 38 
XDY C19 H193 SING N N 39 
XDY N   H    SING N N 40 
XDY N   H2   SING N N 41 
XDY N15 H151 SING N N 42 
XDY C   OXT  SING N N 43 
XDY OXT HXT  SING N N 44 
# 
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 
XDY SMILES           ACDLabs              12.01 "C(CN(C1C(N)CCC1)C(=O)CN2C(NC(=O)C(C)=C2)=O)(O)=O"                                                                                                    
XDY InChI            InChI                1.03  "InChI=1S/C14H20N4O5/c1-8-5-17(14(23)16-13(8)22)6-11(19)18(7-12(20)21)10-4-2-3-9(10)15/h5,9-10H,2-4,6-7,15H2,1H3,(H,20,21)(H,16,22,23)/t9-,10-/m0/s1" 
XDY InChIKey         InChI                1.03  LPWTXUYWYQYXJR-UWVGGRQHSA-N                                                                                                                           
XDY SMILES_CANONICAL CACTVS               3.385 "CC1=CN(CC(=O)N(CC(O)=O)[C@H]2CCC[C@@H]2N)C(=O)NC1=O"                                                                                                 
XDY SMILES           CACTVS               3.385 "CC1=CN(CC(=O)N(CC(O)=O)[CH]2CCC[CH]2N)C(=O)NC1=O"                                                                                                    
XDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)CC(=O)N(CC(=O)O)[C@H]2CCC[C@@H]2N"                                                                                                 
XDY SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)CC(=O)N(CC(=O)O)C2CCCC2N"                                                                                                          
# 
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 
XDY "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine"                    
XDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[[(1~{S},2~{S})-2-azanylcyclopentyl]-[2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-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 
XDY "Create component" 2020-12-11 RCSB 
XDY "Initial release"  2020-12-23 RCSB 
XDY "Modify backbone"  2023-11-03 PDBE 
# 
