data_Y19
# 
_chem_comp.id                                    Y19 
_chem_comp.name                                  "1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             ? 
_chem_comp.formula                               "C12 H20 N4 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-11-27 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        332.310 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y19 
_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        2VI5 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
Y19 O2   O2   O 0 1 N N N 10.113 10.066 -15.178 2.118  -4.055 -0.377 O2   Y19 1  
Y19 C2   C2   C 0 1 N N N 10.001 8.959  -15.748 2.246  -2.871 -0.126 C2   Y19 2  
Y19 N3   N3   N 0 1 N N N 8.990  8.748  -16.624 3.486  -2.410 0.075  N3   Y19 3  
Y19 C4   C4   C 0 1 N N N 8.832  7.573  -17.271 3.718  -1.109 0.359  C4   Y19 4  
Y19 O4   O4   O 0 1 N N N 7.877  7.421  -18.065 4.841  -0.691 0.540  O4   Y19 5  
Y19 N1   N1   N 0 1 N N N 10.903 7.991  -15.482 1.139  -2.127 -0.076 N1   Y19 6  
Y19 C6   C6   C 0 1 N N N 10.850 6.768  -16.067 1.162  -0.841 0.185  C6   Y19 7  
Y19 C5   C5   C 0 1 N N S 9.749  6.435  -17.013 2.510  -0.194 0.439  C5   Y19 8  
Y19 N13  N13  N 0 1 N N N 10.199 5.775  -18.234 2.686  0.881  -0.540 N13  Y19 9  
Y19 C14  C14  C 0 1 N N N 9.783  4.547  -18.571 3.397  1.979  -0.215 C14  Y19 10 
Y19 C15  C15  C 0 1 N N N 8.824  3.831  -17.640 3.579  3.085  -1.222 C15  Y19 11 
Y19 C16  C16  C 0 1 N N N 7.443  3.695  -18.248 4.419  4.205  -0.604 C16  Y19 12 
Y19 O23  O23  O 0 1 N N N 10.162 3.992  -19.588 3.891  2.076  0.888  O23  Y19 13 
Y19 N7   N7   N 0 1 N N N 11.779 5.832  -15.737 0.022  -0.118 0.228  N7   Y19 14 
Y19 C8   C8   C 0 1 N N N 12.864 6.134  -14.812 -1.267 -0.767 -0.021 C8   Y19 15 
Y19 C9   C9   C 0 1 N N S 12.445 5.912  -13.362 -2.389 0.268  0.086  C9   Y19 16 
Y19 O9   O9   O 0 1 N N N 11.623 6.995  -12.916 -2.387 0.838  1.397  O9   Y19 17 
Y19 C10  C10  C 0 1 N N S 13.687 5.849  -12.476 -3.735 -0.410 -0.174 C10  Y19 18 
Y19 O10  O10  O 0 1 N N N 14.591 6.906  -12.828 -3.737 -0.980 -1.484 O10  Y19 19 
Y19 C11  C11  C 0 1 N N R 14.388 4.493  -12.590 -4.857 0.626  -0.066 C11  Y19 20 
Y19 O11  O11  O 0 1 N N N 13.520 3.455  -12.114 -4.855 1.195  1.244  O11  Y19 21 
Y19 C12  C12  C 0 1 N N N 15.707 4.459  -11.822 -6.203 -0.053 -0.326 C12  Y19 22 
Y19 O12  O12  O 0 1 N N N 15.477 4.608  -10.417 -7.238 0.933  -0.342 O12  Y19 23 
Y19 H3   H3   H 0 1 N N N 8.339  9.487  -16.798 4.236  -3.023 0.016  H3   Y19 24 
Y19 H5   H5   H 0 1 N N N 9.146  5.680  -16.486 2.492  0.257  1.431  H5   Y19 25 
Y19 H7   H7   H 0 1 N N N 11.717 4.918  -16.137 0.058  0.832  0.423  H7   Y19 26 
Y19 H13  H13  H 0 1 N N N 10.837 6.254  -18.837 2.291  0.803  -1.423 H13  Y19 27 
Y19 H151 1H15 H 0 0 N N N 9.219  2.825  -17.433 4.086  2.694  -2.104 H151 Y19 28 
Y19 H152 2H15 H 0 0 N N N 8.735  4.424  -16.718 2.603  3.478  -1.509 H152 Y19 29 
Y19 H161 1H16 H 0 0 N N N 6.690  3.662  -17.446 4.550  5.005  -1.333 H161 Y19 30 
Y19 H162 2H16 H 0 0 N N N 7.244  4.557  -18.902 3.911  4.596  0.277  H162 Y19 31 
Y19 H163 3H16 H 0 0 N N N 7.392  2.767  -18.837 5.394  3.811  -0.317 H163 Y19 32 
Y19 H8C1 1H8C H 0 0 N N N 13.716 5.476  -15.039 -1.268 -1.202 -1.020 H8C1 Y19 33 
Y19 H8C2 2H8C H 0 0 N N N 13.137 7.193  -14.934 -1.427 -1.553 0.717  H8C2 Y19 34 
Y19 H9   H9   H 0 1 N N N 11.883 4.969  -13.298 -2.229 1.054  -0.652 H9   Y19 35 
Y19 HA   HA   H 0 1 N N N 11.441 6.894  -11.989 -2.524 0.195  2.105  HA   Y19 36 
Y19 H10  H10  H 0 1 N N N 13.368 5.974  -11.431 -3.895 -1.196 0.565  H10  Y19 37 
Y19 HB   HB   H 0 1 N N N 14.791 7.423  -12.056 -3.600 -0.336 -2.193 HB   Y19 38 
Y19 H11  H11  H 0 1 N N N 14.621 4.330  -13.653 -4.697 1.411  -0.805 H11  Y19 39 
Y19 HC   HC   H 0 1 N N N 13.328 2.852  -12.823 -4.992 0.552  1.953  HC   Y19 40 
Y19 H121 1H12 H 0 0 N N N 16.205 3.495  -12.005 -6.174 -0.563 -1.289 H121 Y19 41 
Y19 H122 2H12 H 0 0 N N N 16.340 5.289  -12.168 -6.404 -0.777 0.463  H122 Y19 42 
Y19 H12  H12  H 0 1 N N N 16.310 4.641  -9.961  -8.121 0.574  -0.502 H12  Y19 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 
Y19 O2  C2   DOUB N N 1  
Y19 C2  N3   SING N N 2  
Y19 C2  N1   SING N N 3  
Y19 N3  C4   SING N N 4  
Y19 C4  O4   DOUB N N 5  
Y19 C4  C5   SING N N 6  
Y19 N1  C6   DOUB N N 7  
Y19 C6  C5   SING N N 8  
Y19 C6  N7   SING N N 9  
Y19 C5  N13  SING N N 10 
Y19 N13 C14  SING N N 11 
Y19 C14 C15  SING N N 12 
Y19 C14 O23  DOUB N N 13 
Y19 C15 C16  SING N N 14 
Y19 N7  C8   SING N N 15 
Y19 C8  C9   SING N N 16 
Y19 C9  O9   SING N N 17 
Y19 C9  C10  SING N N 18 
Y19 C10 O10  SING N N 19 
Y19 C10 C11  SING N N 20 
Y19 C11 O11  SING N N 21 
Y19 C11 C12  SING N N 22 
Y19 C12 O12  SING N N 23 
Y19 N3  H3   SING N N 24 
Y19 C5  H5   SING N N 25 
Y19 N7  H7   SING N N 26 
Y19 N13 H13  SING N N 27 
Y19 C15 H151 SING N N 28 
Y19 C15 H152 SING N N 29 
Y19 C16 H161 SING N N 30 
Y19 C16 H162 SING N N 31 
Y19 C16 H163 SING N N 32 
Y19 C8  H8C1 SING N N 33 
Y19 C8  H8C2 SING N N 34 
Y19 C9  H9   SING N N 35 
Y19 O9  HA   SING N N 36 
Y19 C10 H10  SING N N 37 
Y19 O10 HB   SING N N 38 
Y19 C11 H11  SING N N 39 
Y19 O11 HC   SING N N 40 
Y19 C12 H121 SING N N 41 
Y19 C12 H122 SING N N 42 
Y19 O12 H12  SING N N 43 
# 
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 
Y19 SMILES           ACDLabs              10.04 "O=C1NC(=O)N=C(NCC(O)C(O)C(O)CO)C1NC(=O)CC"                                                                                                                       
Y19 SMILES_CANONICAL CACTVS               3.341 "CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@H](O)[C@H](O)[C@H](O)CO"                                                                                                      
Y19 SMILES           CACTVS               3.341 "CCC(=O)N[CH]1C(=O)NC(=O)N=C1NC[CH](O)[CH](O)[CH](O)CO"                                                                                                           
Y19 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@@H]([C@@H]([C@@H](CO)O)O)O"                                                                                                   
Y19 SMILES           "OpenEye OEToolkits" 1.5.0 "CCC(=O)NC1C(=O)NC(=O)N=C1NCC(C(C(CO)O)O)O"                                                                                                                       
Y19 InChI            InChI                1.03  "InChI=1S/C12H20N4O7/c1-2-7(20)14-8-10(15-12(23)16-11(8)22)13-3-5(18)9(21)6(19)4-17/h5-6,8-9,17-19,21H,2-4H2,1H3,(H,14,20)(H2,13,15,16,22,23)/t5-,6+,8-,9-/m0/s1" 
Y19 InChIKey         InChI                1.03  NPNFNBTUUJYCDD-FAYXRDSDSA-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 
Y19 "SYSTEMATIC NAME" ACDLabs              10.04 "1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol"  
Y19 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(5S)-2,4-dioxo-6-[[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino]-5H-pyrimidin-5-yl]propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y19 "Create component"  2007-11-27 EBI  
Y19 "Modify descriptor" 2011-06-04 RCSB 
# 
