data_YBY
#

_chem_comp.id                                   YBY
_chem_comp.name                                 "N-{[(1S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl]carbamoyl}-L-glutamic acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H17 I N2 O8"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(S)-2-(3-((S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl)ureido)pentanedioic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2008-06-05
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       480.209
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YBY
_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       3D7F
_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
YBY  I18   I18   I  0  1  N  N  N  24.576  49.559  43.654  -3.176  -1.979   0.795  I18   YBY   1  
YBY  C17   C17   C  0  1  Y  N  N  23.879  47.559  43.895  -3.034  -0.015   0.079  C17   YBY   2  
YBY  C16   C16   C  0  1  Y  N  N  22.601  47.239  43.427  -2.162   0.876   0.674  C16   YBY   3  
YBY  C19   C19   C  0  1  Y  N  N  24.643  46.549  44.511  -3.811   0.390  -0.997  C19   YBY   4  
YBY  O20   O20   O  0  1  N  N  N  25.897  46.827  45.013  -4.666  -0.487  -1.588  O20   YBY   5  
YBY  C21   C21   C  0  1  Y  N  N  24.149  45.257  44.644  -3.715   1.691  -1.468  C21   YBY   6  
YBY  C22   C22   C  0  1  Y  N  N  22.867  44.962  44.147  -2.845   2.580  -0.866  C22   YBY   7  
YBY  C15   C15   C  0  1  Y  N  N  22.097  45.947  43.562  -2.068   2.172   0.202  C15   YBY   8  
YBY  C14   C14   C  0  1  N  N  N  20.704  45.646  43.050  -1.117   3.143   0.853  C14   YBY   9  
YBY  C13   C13   C  0  1  N  N  S  19.806  44.995  44.133   0.246   3.064   0.162  C13   YBY  10  
YBY  C23   C23   C  0  1  N  N  N  20.003  45.621  45.487   1.160   4.119   0.730  C23   YBY  11  
YBY  O25   O25   O  0  1  N  N  N  19.551  46.784  45.643   2.194   3.797   1.266  O25   YBY  12  
YBY  O24   O24   O  0  1  N  N  N  20.509  44.920  46.387   0.826   5.416   0.640  O24   YBY  13  
YBY  N12   N12   N  0  1  N  N  N  18.471  45.344  43.644   0.830   1.739   0.385  N12   YBY  14  
YBY  C11   C11   C  0  1  N  N  N  17.827  44.540  42.797   1.731   1.245  -0.487  C11   YBY  15  
YBY  O26   O26   O  0  1  N  N  N  18.234  43.460  42.333   2.059   1.898  -1.459  O26   YBY  16  
YBY  N10   N10   N  0  1  N  N  N  16.580  44.950  42.441   2.269   0.026  -0.282  N10   YBY  17  
YBY  C6    C6    C  0  1  N  N  S  15.905  44.259  41.353   3.248  -0.512  -1.230  C6    YBY  18  
YBY  C7    C7    C  0  1  N  N  N  16.858  44.488  40.163   2.527  -1.181  -2.371  C7    YBY  19  
YBY  O9    O9    O  0  1  N  N  N  17.783  45.378  40.141   3.227  -1.750  -3.366  O9    YBY  20  
YBY  O8    O8    O  0  1  N  N  N  16.774  43.707  39.159   1.319  -1.207  -2.391  O8    YBY  21  
YBY  C5    C5    C  0  1  N  N  N  14.618  45.017  40.910   4.138  -1.533  -0.519  C5    YBY  22  
YBY  C4    C4    C  0  1  N  N  N  14.823  46.551  40.840   4.964  -0.828   0.559  C4    YBY  23  
YBY  C2    C2    C  0  1  N  N  N  13.694  47.331  40.169   5.840  -1.835   1.259  C2    YBY  24  
YBY  O1    O1    O  0  1  N  N  N  12.914  46.732  39.392   5.808  -2.997   0.929  O1    YBY  25  
YBY  O3    O3    O  0  1  N  N  N  13.653  48.576  40.412   6.657  -1.440   2.249  O3    YBY  26  
YBY  H16   H16   H  0  1  N  N  N  21.998  48.001  42.956  -1.554   0.561   1.509  H16   YBY  27  
YBY  HO20  HO20  H  0  0  N  N  N  26.518  46.891  44.297  -5.553  -0.491  -1.203  HO20  YBY  28  
YBY  H21   H21   H  0  1  N  N  N  24.741  44.491  45.122  -4.318   2.008  -2.306  H21   YBY  29  
YBY  H22   H22   H  0  1  N  N  N  22.482  43.956  44.224  -2.770   3.593  -1.233  H22   YBY  30  
YBY  H14   H14   H  0  1  N  N  N  20.238  46.590  42.730  -1.512   4.155   0.763  H14   YBY  31  
YBY  H14A  H14A  H  0  0  N  N  N  20.797  44.935  42.216  -1.004   2.890   1.908  H14A  YBY  32  
YBY  H13   H13   H  0  1  N  N  N  20.007  43.922  44.266   0.120   3.230  -0.908  H13   YBY  33  
YBY  HO24  HO24  H  0  0  N  N  N  20.500  45.401  47.206   1.444   6.055   1.019  HO24  YBY  34  
YBY  HN12  HN12  H  0  0  N  N  N  18.038  46.193  43.948   0.569   1.218   1.160  HN12  YBY  35  
YBY  HN10  HN10  H  0  0  N  N  N  16.137  45.710  42.917   2.008  -0.495   0.494  HN10  YBY  36  
YBY  H6    H6    H  0  1  N  N  N  15.666  43.224  41.640   3.864   0.300  -1.616  H6    YBY  37  
YBY  HO9   HO9   H  0  1  N  N  N  18.278  45.301  39.334   2.720  -2.167  -4.076  HO9   YBY  38  
YBY  H5    H5    H  0  1  N  N  N  14.330  44.659  39.911   3.515  -2.299  -0.057  H5    YBY  39  
YBY  H5A   H5A   H  0  1  N  N  N  13.838  44.818  41.659   4.807  -1.998  -1.243  H5A   YBY  40  
YBY  H4    H4    H  0  1  N  N  N  14.915  46.921  41.872   5.587  -0.063   0.097  H4    YBY  41  
YBY  H4A   H4A   H  0  1  N  N  N  15.718  46.714  40.222   4.294  -0.364   1.283  H4A   YBY  42  
YBY  HO3   HO3   H  0  1  N  N  N  12.946  48.973  39.917   7.200  -2.122   2.668  HO3   YBY  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
YBY  I18  C17   SING  N  N   1  
YBY  C16  C17   DOUB  Y  N   2  
YBY  C17  C19   SING  Y  N   3  
YBY  C16  C15   SING  Y  N   4  
YBY  C16  H16   SING  N  N   5  
YBY  C19  C21   DOUB  Y  N   6  
YBY  C19  O20   SING  N  N   7  
YBY  O20  HO20  SING  N  N   8  
YBY  C22  C21   SING  Y  N   9  
YBY  C21  H21   SING  N  N  10  
YBY  C15  C22   DOUB  Y  N  11  
YBY  C22  H22   SING  N  N  12  
YBY  C14  C15   SING  N  N  13  
YBY  C14  C13   SING  N  N  14  
YBY  C14  H14   SING  N  N  15  
YBY  C14  H14A  SING  N  N  16  
YBY  N12  C13   SING  N  N  17  
YBY  C13  C23   SING  N  N  18  
YBY  C13  H13   SING  N  N  19  
YBY  C23  O25   DOUB  N  N  20  
YBY  C23  O24   SING  N  N  21  
YBY  O24  HO24  SING  N  N  22  
YBY  C11  N12   SING  N  N  23  
YBY  N12  HN12  SING  N  N  24  
YBY  O26  C11   DOUB  N  N  25  
YBY  N10  C11   SING  N  N  26  
YBY  C6   N10   SING  N  N  27  
YBY  N10  HN10  SING  N  N  28  
YBY  C7   C6    SING  N  N  29  
YBY  C5   C6    SING  N  N  30  
YBY  C6   H6    SING  N  N  31  
YBY  O8   C7    DOUB  N  N  32  
YBY  O9   C7    SING  N  N  33  
YBY  O9   HO9   SING  N  N  34  
YBY  C4   C5    SING  N  N  35  
YBY  C5   H5    SING  N  N  36  
YBY  C5   H5A   SING  N  N  37  
YBY  C2   C4    SING  N  N  38  
YBY  C4   H4    SING  N  N  39  
YBY  C4   H4A   SING  N  N  40  
YBY  O1   C2    DOUB  N  N  41  
YBY  C2   O3    SING  N  N  42  
YBY  O3   HO3   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
YBY  SMILES            ACDLabs               10.04  "Ic1cc(ccc1O)CC(C(=O)O)NC(=O)NC(C(=O)O)CCC(=O)O"  
YBY  SMILES_CANONICAL  CACTVS                3.341  "OC(=O)CC[C@H](NC(=O)N[C@@H](Cc1ccc(O)c(I)c1)C(O)=O)C(O)=O"  
YBY  SMILES            CACTVS                3.341  "OC(=O)CC[CH](NC(=O)N[CH](Cc1ccc(O)c(I)c1)C(O)=O)C(O)=O"  
YBY  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1cc(c(cc1C[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)I)O"  
YBY  SMILES            "OpenEye OEToolkits"  1.5.0  "c1cc(c(cc1CC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)I)O"  
YBY  InChI             InChI                 1.03   "InChI=1S/C15H17IN2O8/c16-8-5-7(1-3-11(8)19)6-10(14(24)25)18-15(26)17-9(13(22)23)2-4-12(20)21/h1,3,5,9-10,19H,2,4,6H2,(H,20,21)(H,22,23)(H,24,25)(H2,17,18,26)/t9-,10-/m0/s1"  
YBY  InChIKey          InChI                 1.03   GUNPTUQXZIVQBT-UWVGGRQHSA-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
YBY  "SYSTEMATIC NAME"  ACDLabs               10.04  "N-{[(1S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl]carbamoyl}-L-glutamic acid"  
YBY  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2S)-2-[[(2S)-1-hydroxy-3-(4-hydroxy-3-iodo-phenyl)-1-oxo-propan-2-yl]carbamoylamino]pentanedioic 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
YBY  "Create component"      2008-06-05  RCSB  
YBY  "Modify aromatic_flag"  2011-06-04  RCSB  
YBY  "Modify descriptor"     2011-06-04  RCSB  
YBY  "Modify synonyms"       2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     YBY
_pdbx_chem_comp_synonyms.name        "(S)-2-(3-((S)-1-carboxy-2-(4-hydroxy-3-iodophenyl)ethyl)ureido)pentanedioic acid"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
