data_2L4
#

_chem_comp.id                                   2L4
_chem_comp.name                                 "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H16 N4 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "5-(2-oxoethylideneamino)-6-D-ribitylaminouracil"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-11-25
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       316.267
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    2L4
_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       4NQE
_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
2L4  C4      C4      C  0  1  N  N  N  -92.587  65.644  93.157   3.904   0.742  -0.246  C4      2L4   1  
2L4  C6      C6      C  0  1  N  N  N  -91.503  68.351  92.689   3.507  -2.100   0.323  C6      2L4   2  
2L4  C7      C7      C  0  1  N  N  N  -90.995  69.734  92.411   3.464  -3.507   0.245  C7      2L4   3  
2L4  N1      N1      N  0  1  N  N  N  -90.870  64.087  94.673   1.469   2.005   0.028  N1      2L4   4  
2L4  N3      N3      N  0  1  N  N  N  -92.926  64.395  93.553   3.818   2.080  -0.097  N3      2L4   5  
2L4  N5      N5      N  0  1  N  N  N  -90.777  67.473  93.233   2.689  -1.379  -0.404  N5      2L4   6  
2L4  C4A     C4A     C  0  1  N  N  N  -91.249  66.184  93.522   2.662  -0.045  -0.259  C4A     2L4   7  
2L4  O4      O4      O  0  1  N  N  N  -93.399  66.347  92.512   4.986   0.199  -0.371  O4      2L4   8  
2L4  C2      C2      C  0  1  N  N  N  -92.108  63.661  94.317   2.626   2.685   0.035  C2      2L4   9  
2L4  O2      O2      O  0  1  N  N  N  -92.438  62.503  94.622   2.595   3.893   0.166  O2      2L4  10  
2L4  C8A     C8A     C  0  1  N  N  N  -90.407  65.302  94.333   1.444   0.647  -0.116  C8A     2L4  11  
2L4  N8      N8      N  0  1  N  N  N  -89.213  65.769  94.737   0.261  -0.027  -0.120  N8      2L4  12  
2L4  "C1'"   "C1'"   C  0  1  N  N  N  -88.543  65.322  95.932  -0.999   0.705   0.030  "C1'"   2L4  13  
2L4  "C2'"   "C2'"   C  0  1  N  N  S  -87.408  64.367  95.580  -2.169  -0.281  -0.008  "C2'"   2L4  14  
2L4  "O2'"   "O2'"   O  0  1  N  N  N  -86.458  65.002  94.702  -2.167  -0.974  -1.258  "O2'"   2L4  15  
2L4  "C3'"   "C3'"   C  0  1  N  N  S  -87.870  62.994  95.052  -3.485   0.484   0.149  "C3'"   2L4  16  
2L4  "O3'"   "O3'"   O  0  1  N  N  N  -88.915  62.422  95.852  -3.487   1.177   1.398  "O3'"   2L4  17  
2L4  "C4'"   "C4'"   C  0  1  N  N  R  -86.726  62.003  94.984  -4.655  -0.502   0.110  "C4'"   2L4  18  
2L4  "O4'"   "O4'"   O  0  1  N  N  N  -87.203  60.831  94.330  -4.653  -1.195  -1.139  "O4'"   2L4  19  
2L4  "C5'"   "C5'"   C  0  1  N  N  N  -86.109  61.683  96.348  -5.971   0.262   0.267  "C5'"   2L4  20  
2L4  "O5'"   "O5'"   O  0  1  N  N  N  -85.086  60.687  96.214  -7.054  -0.666   0.348  "O5'"   2L4  21  
2L4  H1      H1      H  0  1  N  N  N  -92.517  68.099  92.417   4.213  -1.617   0.981  H1      2L4  22  
2L4  O1      O1      O  0  1  N  Y  N  -91.263  71.073  92.835   4.222  -4.176   0.919  O1      2L4  23  
2L4  H5      H5      H  0  1  N  N  N  -93.805  64.013  93.269   4.629   2.613  -0.086  H5      2L4  24  
2L4  H7      H7      H  0  1  N  N  N  -88.580  65.586  93.985   0.253  -0.991  -0.223  H7      2L4  25  
2L4  H8      H8      H  0  1  N  N  N  -88.132  66.193  96.464  -1.001   1.234   0.983  H8      2L4  26  
2L4  H9      H9      H  0  1  N  N  N  -89.265  64.803  96.580  -1.102   1.423  -0.784  H9      2L4  27  
2L4  H10     H10     H  0  1  N  N  N  -86.882  64.162  96.524  -2.066  -0.998   0.805  H10     2L4  28  
2L4  H11     H11     H  0  1  N  N  N  -85.760  64.392  94.495  -2.255  -0.396  -2.028  H11     2L4  29  
2L4  H12     H12     H  0  1  N  N  N  -88.247  63.143  94.029  -3.588   1.201  -0.665  H12     2L4  30  
2L4  H13     H13     H  0  1  N  N  N  -89.167  61.580  95.490  -3.399   0.599   2.169  H13     2L4  31  
2L4  H14     H14     H  0  1  N  N  N  -85.936  62.453  94.365  -4.552  -1.220   0.924  H14     2L4  32  
2L4  H15     H15     H  0  1  N  N  N  -86.503  60.192  94.274  -4.741  -0.617  -1.910  H15     2L4  33  
2L4  H16     H16     H  0  1  N  N  N  -85.670  62.599  96.771  -5.937   0.861   1.177  H16     2L4  34  
2L4  H17     H17     H  0  1  N  N  N  -86.894  61.308  97.021  -6.116   0.916  -0.593  H17     2L4  35  
2L4  H18     H18     H  0  1  N  N  N  -84.713  60.499  97.067  -7.921  -0.251   0.449  H18     2L4  36  
2L4  H2      H2      H  0  1  N  N  N  -90.199  69.713  91.682   2.757  -3.991  -0.413  H2      2L4  37  
2L4  H161    H161    H  0  0  N  N  N  -90.283  63.477  95.206   0.634   2.488   0.128  H161    2L4  38  
#   #
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
2L4  C4     C4A     SING  N  N   1  
2L4  C4     N3      SING  N  N   2  
2L4  C6     N5      DOUB  N  N   3  
2L4  C6     H1      SING  N  N   4  
2L4  C7     C6      SING  N  N   5  
2L4  C7     O1      DOUB  N  N   6  
2L4  N3     C2      SING  N  N   7  
2L4  N3     H5      SING  N  N   8  
2L4  N5     C4A     SING  N  N   9  
2L4  C4A    C8A     DOUB  N  N  10  
2L4  O4     C4      DOUB  N  N  11  
2L4  C2     O2      DOUB  N  N  12  
2L4  C2     N1      SING  N  N  13  
2L4  C8A    N1      SING  N  N  14  
2L4  C8A    N8      SING  N  N  15  
2L4  N8     "C1'"   SING  N  N  16  
2L4  N8     H7      SING  N  N  17  
2L4  "C1'"  H8      SING  N  N  18  
2L4  "C1'"  H9      SING  N  N  19  
2L4  "C2'"  "C1'"   SING  N  N  20  
2L4  "C2'"  H10     SING  N  N  21  
2L4  "O2'"  "C2'"   SING  N  N  22  
2L4  "O2'"  H11     SING  N  N  23  
2L4  "C3'"  "C2'"   SING  N  N  24  
2L4  "C3'"  "O3'"   SING  N  N  25  
2L4  "C3'"  H12     SING  N  N  26  
2L4  "O3'"  H13     SING  N  N  27  
2L4  "C4'"  "C3'"   SING  N  N  28  
2L4  "C4'"  "C5'"   SING  N  N  29  
2L4  "C4'"  H14     SING  N  N  30  
2L4  "O4'"  "C4'"   SING  N  N  31  
2L4  "O4'"  H15     SING  N  N  32  
2L4  "C5'"  H16     SING  N  N  33  
2L4  "C5'"  H17     SING  N  N  34  
2L4  "O5'"  "C5'"   SING  N  N  35  
2L4  "O5'"  H18     SING  N  N  36  
2L4  C7     H2      SING  N  N  37  
2L4  N1     H161    SING  N  N  38  
#   #
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
2L4  SMILES            ACDLabs               12.01  "O=C1NC(NCC(O)C(O)C(O)CO)=C(\N=C\C=O)C(=O)N1"  
2L4  InChI             InChI                 1.03   "InChI=1S/C11H16N4O7/c16-2-1-12-7-9(14-11(22)15-10(7)21)13-3-5(18)8(20)6(19)4-17/h1-2,5-6,8,17-20H,3-4H2,(H3,13,14,15,21,22)/b12-1+/t5-,6+,8-/m0/s1"  
2L4  InChIKey          InChI                 1.03   PUEQUELBQOQOOV-GJQDMXJLSA-N  
2L4  SMILES_CANONICAL  CACTVS                3.370  "OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(N=CC=O)C(=O)NC(=O)N1"  
2L4  SMILES            CACTVS                3.370  "OC[CH](O)[CH](O)[CH](O)CNC1=C(N=CC=O)C(=O)NC(=O)N1"  
2L4  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C(C(C(C(CO)O)O)O)NC1=C(C(=O)NC(=O)N1)/N=C/C=O"  
2L4  SMILES            "OpenEye OEToolkits"  1.7.6  "C(C(C(C(CO)O)O)O)NC1=C(C(=O)NC(=O)N1)N=CC=O"  
#   #
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
2L4  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol"  
2L4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "(2E)-2-[[2,4-bis(oxidanylidene)-6-[2,3,4,5-tetrakis(oxidanyl)pentylamino]-1H-pyrimidin-5-yl]imino]ethanal"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2L4  "Create component"  2013-11-25  RCSB  
2L4  "Initial release"   2014-04-16  RCSB  
2L4  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     2L4
_pdbx_chem_comp_synonyms.name        "5-(2-oxoethylideneamino)-6-D-ribitylaminouracil"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
