data_CUD
# 
_chem_comp.id                                    CUD 
_chem_comp.name                                  "3-(4-amino-2-oxopyrimidin-1(2H)-yl)-D-alanine" 
_chem_comp.type                                  "D-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C7 H10 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2008-02-12 
_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                        198.179 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CUD 
_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        3C1P 
_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 
CUD C2   C2   C 0 1 N N N N N N 1.143 -13.154 4.996 -1.163 -0.834 -0.429 C2   CUD 1  
CUD C4   C4   C 0 1 N N N N N N 1.601 -14.436 3.111 -3.149 0.185  0.167  C4   CUD 2  
CUD C5   C5   C 0 1 N N N N N N 2.600 -13.550 2.632 -2.505 1.439  0.161  C5   CUD 3  
CUD C6   C6   C 0 1 N N N N N N 2.849 -12.484 3.417 -1.189 1.499  -0.152 C6   CUD 4  
CUD N    N    N 0 1 N N N Y Y N 0.637 -9.668  4.675 1.347  -0.973 1.191  N    CUD 5  
CUD CA   CA   C 0 1 N N R Y N N 2.102 -9.790  4.655 1.737  0.256  0.486  CA   CUD 6  
CUD CB   CB   C 0 1 N N N N N N 2.428 -11.101 5.379 0.903  0.400  -0.788 CB   CUD 7  
CUD N1   N1   N 0 1 N N N N N N 2.141 -12.284 4.564 -0.521 0.349  -0.448 N1   CUD 8  
CUD N4   N4   N 0 1 N N N N N N 1.367 -15.574 2.464 -4.486 0.095  0.475  N4   CUD 9  
CUD N3   N3   N 0 1 N N N N N N 0.833 -14.218 4.211 -2.458 -0.909 -0.128 N3   CUD 10 
CUD O2   O2   O 0 1 N N N N N N 0.535 -12.931 6.037 -0.549 -1.854 -0.696 O2   CUD 11 
CUD C    C    C 0 1 N N N Y N Y 2.738 -8.642  5.437 3.199  0.185  0.125  C    CUD 12 
CUD O    O    O 0 1 N N N Y N Y 2.110 -8.085  6.335 3.760  -0.884 0.084  O    CUD 13 
CUD OXT  OXT  O 0 1 N Y N Y N Y 3.970 -8.365  5.073 3.877  1.310  -0.152 OXT  CUD 14 
CUD H    HN   H 0 1 N N N Y Y N 0.317 -9.640  5.622 1.498  -1.785 0.612  HN   CUD 15 
CUD HA   HA   H 0 1 N N N Y N N 2.482 -9.768  3.623 1.564  1.116  1.133  HA   CUD 16 
CUD HB   HB   H 0 1 N N N N N N 3.499 -11.103 5.628 1.129  1.354  -1.264 HB   CUD 17 
CUD HBA  HBA  H 0 1 N N N N N N 1.795 -11.153 6.277 1.142  -0.414 -1.473 HBA  CUD 18 
CUD H6   H6   H 0 1 N N N N N N 3.618 -11.780 3.134 -0.673 2.448  -0.163 H6   CUD 19 
CUD H5   H5   H 0 1 N N N N N N 3.124 -13.718 1.703 -3.054 2.338  0.398  H5   CUD 20 
CUD HN4  HN4  H 0 1 N N N N N N 0.686 -16.258 2.725 -4.927 -0.769 0.478  HN4  CUD 21 
CUD HN4A HN4A H 0 0 N N N N N N 1.978 -15.639 1.675 -4.989 0.896  0.690  HN4A CUD 22 
CUD H2   HNA  H 0 1 N Y N Y Y N 0.366 -8.827  4.207 1.838  -1.058 2.068  HNA  CUD 23 
CUD HXT  HXT  H 0 1 N Y N Y N Y 4.310 -7.661  5.613 4.812  1.214  -0.379 HXT  CUD 24 
# 
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 
CUD N3   C2  SING N N 1  
CUD N1   C2  SING N N 2  
CUD C2   O2  DOUB N N 3  
CUD N4   C4  SING N N 4  
CUD C5   C4  SING N N 5  
CUD C4   N3  DOUB N N 6  
CUD H5   C5  SING N N 7  
CUD C5   C6  DOUB N N 8  
CUD H6   C6  SING N N 9  
CUD C6   N1  SING N N 10 
CUD CA   N   SING N N 11 
CUD N    H   SING N N 12 
CUD N    H2  SING N N 13 
CUD HA   CA  SING N N 14 
CUD CA   CB  SING N N 15 
CUD CA   C   SING N N 16 
CUD N1   CB  SING N N 17 
CUD CB   HB  SING N N 18 
CUD CB   HBA SING N N 19 
CUD HN4A N4  SING N N 20 
CUD N4   HN4 SING N N 21 
CUD OXT  C   SING N N 22 
CUD C    O   DOUB N N 23 
CUD OXT  HXT SING N N 24 
# 
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 
CUD SMILES           ACDLabs              10.04 "O=C1N=C(C=CN1CC(C(=O)O)N)N"                                                                            
CUD SMILES_CANONICAL CACTVS               3.341 "N[C@H](CN1C=CC(=NC1=O)N)C(O)=O"                                                                        
CUD SMILES           CACTVS               3.341 "N[CH](CN1C=CC(=NC1=O)N)C(O)=O"                                                                         
CUD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C[C@H](C(=O)O)N"                                                                      
CUD SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)CC(C(=O)O)N"                                                                          
CUD InChI            InChI                1.03  "InChI=1S/C7H10N4O3/c8-4(6(12)13)3-11-2-1-5(9)10-7(11)14/h1-2,4H,3,8H2,(H,12,13)(H2,9,10,14)/t4-/m1/s1" 
CUD InChIKey         InChI                1.03  XRUZZWBPZICCSB-SCSAIBSYSA-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 
CUD "SYSTEMATIC NAME" ACDLabs              10.04 "3-(4-amino-2-oxopyrimidin-1(2H)-yl)-D-alanine"               
CUD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-3-(4-amino-2-oxo-pyrimidin-1-yl)propanoic 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 
CUD "Create component"  2008-02-12 RCSB 
CUD "Modify descriptor" 2011-06-04 RCSB 
CUD "Modify backbone"   2023-11-03 PDBE 
CUD "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            CUD 
_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" 
_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      ? 
# 
