data_D5Y
#

_chem_comp.id                                   D5Y
_chem_comp.name                                 "methyl 3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alaninate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C8 H10 Br N3 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-20
_chem_comp.pdbx_modified_date                   2020-04-17
_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                       292.087
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D5Y
_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       5QB6
_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.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
D5Y  O3   O1   O   0  1  N  N  N  -3.601   3.122   5.359   0.937  -2.647   0.522  O3   D5Y   1  
D5Y  C4   C1   C   0  1  N  N  N  -3.205   1.581   8.507  -0.650   0.426   0.379  C4   D5Y   2  
D5Y  C5   C2   C   0  1  N  N  N  -2.960   2.631   9.302  -1.915   0.038   0.109  C5   D5Y   3  
D5Y  C6   C3   C   0  1  N  N  N  -2.940   3.974   8.771  -2.199  -1.344  -0.021  C6   D5Y   4  
D5Y  N1   N1   N   0  1  N  N  N  -3.185   4.021   7.410  -1.203  -2.240   0.127  N1   D5Y   5  
D5Y  C7   C4   C   0  1  N  N  N  -3.425   2.964   6.560   0.049  -1.826   0.396  C7   D5Y   6  
D5Y  N2   N2   N   0  1  N  N  N  -5.962   1.113   5.632   2.369  -1.094  -1.339  N2   D5Y   7  
D5Y  BR   BR1  BR  0  0  N  N  N  -2.606   2.394  11.141  -3.289   1.322  -0.091  BR   D5Y   8  
D5Y  O2   O2   O   0  1  N  N  N  -2.731   5.007   9.408  -3.332  -1.718  -0.263  O2   D5Y   9  
D5Y  N    N3   N   0  1  N  N  N  -3.427   1.725   7.158   0.333  -0.517   0.517  N    D5Y  10  
D5Y  C3   C5   C   0  1  N  N  N  -3.606   0.561   6.284   1.708  -0.096   0.797  C3   D5Y  11  
D5Y  C2   C6   C   0  1  N  N  S  -5.080   0.051   6.189   2.454   0.123  -0.521  C2   D5Y  12  
D5Y  C1   C7   C   0  1  N  N  N  -5.623  -0.349   7.547   3.899   0.436  -0.234  C1   D5Y  13  
D5Y  O1   O3   O   0  1  N  N  N  -6.680   0.008   7.982   4.737  -0.429  -0.337  O1   D5Y  14  
D5Y  O    O4   O   0  1  N  N  N  -4.760  -1.129   8.191   4.257   1.676   0.135  O    D5Y  15  
D5Y  C    C8   C   0  1  N  N  N  -5.125  -1.494   9.543   5.667   1.905   0.395  C    D5Y  16  
D5Y  H1   H1   H   0  1  N  N  N  -3.229   0.591   8.939  -0.414   1.475   0.481  H1   D5Y  17  
D5Y  H2   H2   H   0  1  N  N  N  -3.188   4.930   6.994  -1.390  -3.188   0.040  H2   D5Y  18  
D5Y  H3   H3   H   0  1  N  N  N  -6.901   0.773   5.577   2.798  -0.954  -2.241  H3   D5Y  19  
D5Y  H4   H4   H   0  1  N  N  N  -5.933   1.916   6.227   2.782  -1.881  -0.860  H4   D5Y  20  
D5Y  H6   H6   H   0  1  N  N  N  -2.982  -0.259   6.669   1.695   0.834   1.366  H6   D5Y  21  
D5Y  H7   H7   H   0  1  N  N  N  -3.270   0.834   5.273   2.214  -0.868   1.377  H7   D5Y  22  
D5Y  H8   H8   H   0  1  N  N  N  -5.101  -0.825   5.524   2.001   0.955  -1.060  H8   D5Y  23  
D5Y  H9   H9   H   0  1  N  N  N  -4.343  -2.136   9.974   5.999   1.252   1.202  H9   D5Y  24  
D5Y  H10  H10  H   0  1  N  N  N  -5.230  -0.584  10.153   6.242   1.691  -0.506  H10  D5Y  25  
D5Y  H11  H11  H   0  1  N  N  N  -6.080  -2.039   9.530   5.819   2.945   0.683  H11  D5Y  26  
#   #
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
D5Y  O3  C7   DOUB  N  N   1  
D5Y  N2  C2   SING  N  N   2  
D5Y  C2  C3   SING  N  N   3  
D5Y  C2  C1   SING  N  N   4  
D5Y  C3  N    SING  N  N   5  
D5Y  C7  N    SING  N  N   6  
D5Y  C7  N1   SING  N  N   7  
D5Y  N   C4   SING  N  N   8  
D5Y  N1  C6   SING  N  N   9  
D5Y  C1  O1   DOUB  N  N  10  
D5Y  C1  O    SING  N  N  11  
D5Y  O   C    SING  N  N  12  
D5Y  C4  C5   DOUB  N  N  13  
D5Y  C6  C5   SING  N  N  14  
D5Y  C6  O2   DOUB  N  N  15  
D5Y  C5  BR   SING  N  N  16  
D5Y  C4  H1   SING  N  N  17  
D5Y  N1  H2   SING  N  N  18  
D5Y  N2  H3   SING  N  N  19  
D5Y  N2  H4   SING  N  N  20  
D5Y  C3  H6   SING  N  N  21  
D5Y  C3  H7   SING  N  N  22  
D5Y  C2  H8   SING  N  N  23  
D5Y  C   H9   SING  N  N  24  
D5Y  C   H10  SING  N  N  25  
D5Y  C   H11  SING  N  N  26  
#   #
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
D5Y  SMILES            ACDLabs               12.01  "O=C1NC(C(=CN1CC(N)C(=O)OC)Br)=O"  
D5Y  InChI             InChI                 1.03   "InChI=1S/C8H10BrN3O4/c1-16-7(14)5(10)3-12-2-4(9)6(13)11-8(12)15/h2,5H,3,10H2,1H3,(H,11,13,15)/t5-/m0/s1"  
D5Y  InChIKey          InChI                 1.03   SWCNOWRHWSFLMA-YFKPBYRVSA-N  
D5Y  SMILES_CANONICAL  CACTVS                3.385  "COC(=O)[C@@H](N)CN1C=C(Br)C(=O)NC1=O"  
D5Y  SMILES            CACTVS                3.385  "COC(=O)[CH](N)CN1C=C(Br)C(=O)NC1=O"  
D5Y  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "COC(=O)[C@H](CN1C=C(C(=O)NC1=O)Br)N"  
D5Y  SMILES            "OpenEye OEToolkits"  2.0.6  "COC(=O)C(CN1C=C(C(=O)NC1=O)Br)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
D5Y  "SYSTEMATIC NAME"  ACDLabs               12.01  "methyl 3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alaninate"  
D5Y  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "methyl (2~{S})-2-azanyl-3-[5-bromanyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]propanoate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D5Y  "Create component"  2017-10-20  RCSB  
D5Y  "Initial release"   2020-04-22  RCSB  
##
