data_40T
# 
_chem_comp.id                                    40T 
_chem_comp.name                                  "N-[(2S)-2-aminopropyl]-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                               "C12 H18 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-04-26 
_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                        298.295 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     40T 
_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        2KVJ 
_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 
40T C      "C'"   C 0 1 N N N Y N Y 33.527 32.268 41.018 -2.952 -2.130 0.390  "C'"   40T 1  
40T N1     N1     N 0 1 N N N N N N 30.933 27.239 40.759 1.535  -0.454 0.386  N1     40T 2  
40T C2     C2     C 0 1 N N N N N N 30.815 27.098 39.371 2.109  -1.166 -0.600 C2     40T 3  
40T O2     O2     O 0 1 N N N N N N 31.678 27.426 38.569 1.459  -2.012 -1.185 O2     40T 4  
40T N3     N3     N 0 1 N N N N N N 29.674 26.554 38.898 3.391  -0.955 -0.950 N3     40T 5  
40T C4     C4     C 0 1 N N N N N N 28.604 26.200 39.647 4.125  -0.021 -0.312 C4     40T 6  
40T O4     O4     O 0 1 N N N N N N 27.638 25.736 39.055 5.285  0.170  -0.628 O4     40T 7  
40T C5     C5     C 0 1 N N N N N N 28.746 26.407 41.087 3.534  0.735  0.729  C5     40T 8  
40T C6     C6     C 0 1 N N N N N N 29.898 26.907 41.596 2.243  0.507  1.055  C6     40T 9  
40T C7     C7     C 0 1 N N N N N N 27.626 26.046 42.046 4.332  1.785  1.458  C7     40T 10 
40T N      "N1'"  N 0 1 N N N Y Y N 33.843 28.439 44.435 -1.902 2.917  0.319  "N1'"  40T 11 
40T O      "O1'"  O 0 1 N N N Y N Y 33.260 33.449 41.150 -2.688 -2.287 -0.779 "O1'"  40T 12 
40T CA     "C2'"  C 0 1 N N S Y N N 34.881 29.115 43.718 -3.198 2.302  0.002  "C2'"  40T 13 
40T C2M    C2M    C 0 1 N N N N N N 36.139 28.308 43.912 -4.004 3.247  -0.892 C2M    40T 14 
40T "C3'"  "C3'"  C 0 1 N N N Y N N 34.583 29.231 42.223 -2.969 0.979  -0.730 "C3'"  40T 15 
40T "N4'"  "N4'"  N 0 1 N N N Y N N 33.311 29.907 41.925 -2.097 0.120  0.075  "N4'"  40T 16 
40T "C5'"  "C5'"  C 0 1 N N N Y N N 33.305 31.355 42.201 -2.679 -0.804 1.052  "C5'"  40T 17 
40T "C7'"  "C7'"  C 0 1 N N N N N N 32.198 29.294 41.466 -0.760 0.179  -0.084 "C7'"  40T 18 
40T "O7'"  "O7'"  O 0 1 N N N N N N 31.194 29.932 41.162 -0.279 0.943  -0.893 "O7'"  40T 19 
40T "C8'"  "C8'"  C 0 1 N N N N N N 32.196 27.779 41.333 0.137  -0.705 0.744  "C8'"  40T 20 
40T HN3    HN3    H 0 1 N N N N N N 29.614 26.400 37.912 3.789  -1.478 -1.664 HN3    40T 21 
40T H6     H6     H 0 1 N N N N N N 30.002 27.044 42.662 1.774  1.077  1.844  H6     40T 22 
40T H      "HN1'" H 0 0 N N N Y Y N 33.733 27.515 44.069 -1.372 3.099  -0.520 "HN1'" 40T 23 
40T HA     "H22'" H 0 0 N N N Y N N 34.975 30.142 44.102 -3.748 2.117  0.924  "H22'" 40T 24 
40T "H13'" "H13'" H 0 0 N N N Y N N 35.394 29.809 41.757 -3.926 0.480  -0.887 "H13'" 40T 25 
40T "H23'" "H23'" H 0 0 N N N Y N N 34.536 28.215 41.804 -2.498 1.173  -1.694 "H23'" 40T 26 
40T "H15'" "H15'" H 0 0 N N N Y N N 34.114 31.552 42.920 -3.612 -0.389 1.433  "H15'" 40T 27 
40T "H25'" "H25'" H 0 0 N N N Y N N 32.319 31.602 42.621 -1.981 -0.947 1.877  "H25'" 40T 28 
40T H7     H7     H 0 1 N N N N N N 26.726 26.626 41.793 3.853  2.757  1.334  H7     40T 29 
40T H7A    H7A    H 0 1 N N N N N N 27.405 24.971 41.964 4.377  1.536  2.518  H7A    40T 30 
40T H7B    H7B    H 0 1 N N N N N N 27.935 26.279 43.076 5.342  1.822  1.050  H7B    40T 31 
40T "HXT'" "HXT'" H 0 0 N N N N N N 32.331 27.346 42.335 -0.105 -1.750 0.552  "HXT'" 40T 32 
40T "H28'" "H28'" H 0 0 N N N N N N 33.025 27.491 40.670 -0.013 -0.486 1.801  "H28'" 40T 33 
40T H2M    H2M    H 0 1 N N N N N N 36.377 28.252 44.985 -4.966 2.791  -1.128 H2M    40T 34 
40T H2MA   H2MA   H 0 0 N N N N N N 35.988 27.293 43.517 -4.167 4.190  -0.370 H2MA   40T 35 
40T H2MB   H2MB   H 0 0 N N N N N N 36.970 28.790 43.377 -3.454 3.432  -1.814 H2MB   40T 36 
40T OXT    OXT    O 0 1 N Y N Y N Y 34.035 31.762 39.781 -3.494 -3.134 1.097  OXT    40T 37 
40T H2     HNXT   H 0 0 N Y N Y Y N 32.985 28.942 44.334 -2.024 3.760  0.860  HNXT   40T 38 
40T HXT    HXT    H 0 1 N Y N Y N Y 34.110 32.472 39.155 -3.654 -3.964 0.628  HXT    40T 39 
# 
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 
40T C      O      DOUB N N 1  
40T C      "C5'"  SING N N 2  
40T C      OXT    SING N N 3  
40T N1     "C8'"  SING N N 4  
40T N1     C6     SING N N 5  
40T C2     N1     SING N N 6  
40T O2     C2     DOUB N N 7  
40T N3     C2     SING N N 8  
40T N3     C4     SING N N 9  
40T C4     C5     SING N N 10 
40T O4     C4     DOUB N N 11 
40T C5     C6     DOUB N N 12 
40T C5     C7     SING N N 13 
40T C6     H6     SING N N 14 
40T C7     H7B    SING N N 15 
40T N      H2     SING N N 16 
40T CA     N      SING N N 17 
40T CA     C2M    SING N N 18 
40T CA     HA     SING N N 19 
40T C2M    H2MB   SING N N 20 
40T "C3'"  CA     SING N N 21 
40T "N4'"  "C3'"  SING N N 22 
40T "N4'"  "C5'"  SING N N 23 
40T "C5'"  "H15'" SING N N 24 
40T "C5'"  "H25'" SING N N 25 
40T "C7'"  "N4'"  SING N N 26 
40T "O7'"  "C7'"  DOUB N N 27 
40T "C8'"  "C7'"  SING N N 28 
40T "C8'"  "HXT'" SING N N 29 
40T HN3    N3     SING N N 30 
40T H      N      SING N N 31 
40T "H13'" "C3'"  SING N N 32 
40T "H23'" "C3'"  SING N N 33 
40T H7     C7     SING N N 34 
40T H7A    C7     SING N N 35 
40T "H28'" "C8'"  SING N N 36 
40T H2M    C2M    SING N N 37 
40T H2MA   C2M    SING N N 38 
40T OXT    HXT    SING N N 39 
# 
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 
40T SMILES           ACDLabs              12.01 "O=C(N(CC(=O)O)CC(N)C)CN1C=C(C(=O)NC1=O)C"                                                                                          
40T SMILES_CANONICAL CACTVS               3.370 "C[C@H](N)CN(CC(O)=O)C(=O)CN1C=C(C)C(=O)NC1=O"                                                                                      
40T SMILES           CACTVS               3.370 "C[CH](N)CN(CC(O)=O)C(=O)CN1C=C(C)C(=O)NC1=O"                                                                                       
40T SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)CC(=O)N(C[C@H](C)N)CC(=O)O"                                                                                      
40T SMILES           "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)CC(=O)N(CC(C)N)CC(=O)O"                                                                                          
40T InChI            InChI                1.03  "InChI=1S/C12H18N4O5/c1-7-3-16(12(21)14-11(7)20)5-9(17)15(4-8(2)13)6-10(18)19/h3,8H,4-6,13H2,1-2H3,(H,18,19)(H,14,20,21)/t8-/m0/s1" 
40T InChIKey         InChI                1.03  LMRWZEVJIJNHDI-QMMMGPOBSA-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 
40T "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(2S)-2-aminopropyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine"  
40T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "2-[[(2S)-2-azanylpropyl]-[2-(5-methyl-2,4-dioxo-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 
40T "Create component"  2010-04-26 RCSB 
40T "Modify descriptor" 2011-06-04 RCSB 
40T "Modify backbone"   2023-11-03 PDBE 
40T "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            40T 
_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      ? 
# 
