data_DYM
#

_chem_comp.id                                   DYM
_chem_comp.name                                 "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid"
_chem_comp.type                                 L-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C11 H17 N O8"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID; 2,3-DIHYDROXYPROPYL ETHER
MIMETIC; (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enosiduronic acid;
(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-L-threo-hex-4-enosiduronic acid; (2R)-2,3-dihydroxypropyl
2-acetamido-2,4-dideoxy-threo-hex-4-enosiduronic acid
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-11-28
_chem_comp.pdbx_modified_date                   2020-07-17
_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                       291.255
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    DYM
_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       2F13
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  DYM  "6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID"   PDB  ?  
2  DYM  "2,3-DIHYDROXYPROPYL ETHER MIMETIC"                                                       PDB  ?  
3  DYM  "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enosiduronic acid"  PDB  ?  
4  DYM  "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-L-threo-hex-4-enosiduronic acid"        PDB  ?  
5  DYM  "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-threo-hex-4-enosiduronic acid"          PDB  ?  
#   #
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
DYM  C1    C1    C  0  1  N  N  N  77.991  30.365  24.640   1.807   3.286  -0.111  C1    DYM   1  
DYM  C2    C2    C  0  1  N  N  N  77.516  30.208  25.973   1.587   1.842   0.079  C2    DYM   2  
DYM  C3    C3    C  0  1  N  N  N  76.680  31.309  26.690   2.631   1.075   0.358  C3    DYM   3  
DYM  C4    C4    C  0  1  N  N  S  76.274  30.879  28.168   2.504  -0.408   0.577  C4    DYM   4  
DYM  C5    C5    C  0  1  N  N  R  77.318  29.943  28.807   1.166  -0.894   0.010  C5    DYM   5  
DYM  C6    C6    C  0  1  N  N  R  77.429  28.672  27.911   0.064   0.058   0.495  C6    DYM   6  
DYM  C7    C7    C  0  1  N  N  N  78.638  26.398  27.603  -2.314   0.354   0.530  C7    DYM   7  
DYM  C8    C8    C  0  1  N  N  R  79.711  25.471  28.185  -3.617  -0.226  -0.024  C8    DYM   8  
DYM  C9    C9    C  0  1  N  N  N  81.047  25.908  28.038  -4.807   0.504   0.602  C9    DYM   9  
DYM  C10   C10   C  0  1  N  N  N  77.454  29.804  31.356   1.403  -3.313  -0.168  C10   DYM  10  
DYM  C11   C11   C  0  1  N  N  N  76.732  29.336  32.597   1.121  -4.709   0.323  C11   DYM  11  
DYM  N5    N5    N  0  1  N  N  N  76.859  29.598  30.177   0.891  -2.252   0.487  N5    DYM  12  
DYM  O1A   O1A   O  0  1  N  N  N  78.715  29.382  24.031   2.926   3.749  -0.012  O1A   DYM  13  
DYM  O1B   O1B   O  0  1  N  N  N  77.749  31.429  23.968   0.767   4.094  -0.401  O1B   DYM  14  
DYM  O4    O4    O  0  1  N  N  N  76.137  32.092  28.952   3.575  -1.081  -0.087  O4    DYM  15  
DYM  O6    O6    O  0  1  N  N  N  77.843  29.040  26.543   0.326   1.359  -0.033  O6    DYM  16  
DYM  O7    O7    O  0  1  N  N  N  78.471  27.683  28.439  -1.208  -0.404   0.036  O7    DYM  17  
DYM  O8    O8    O  0  1  N  N  N  79.655  25.321  29.539  -3.648  -0.058  -1.443  O8    DYM  18  
DYM  O9    O9    O  0  1  N  N  N  82.115  25.186  28.504  -6.023  -0.113   0.175  O9    DYM  19  
DYM  O10   O10   O  0  1  N  N  N  78.687  30.419  31.510   2.092  -3.143  -1.152  O10   DYM  20  
DYM  H3    H3    H  0  1  N  N  N  76.408  32.252  26.238   3.608   1.531   0.430  H3    DYM  21  
DYM  H4    H4    H  0  1  N  N  N  75.310  30.352  28.119   2.546  -0.623   1.644  H4    DYM  22  
DYM  H5    H5    H  0  1  N  N  N  78.294  30.449  28.846   1.204  -0.887  -1.079  H5    DYM  23  
DYM  H6    H6    H  0  1  N  N  N  76.448  28.176  27.881   0.068   0.099   1.585  H6    DYM  24  
DYM  H71   H71   H  0  1  N  N  N  78.926  26.676  26.578  -2.215   1.392   0.213  H71   DYM  25  
DYM  H72   H72   H  0  1  N  N  N  77.678  25.861  27.581  -2.329   0.306   1.619  H72   DYM  26  
DYM  H8    H8    H  0  1  N  N  N  79.600  24.491  27.698  -3.675  -1.287   0.218  H8    DYM  27  
DYM  H91   H91   H  0  1  N  N  N  81.210  26.032  26.957  -4.735   0.451   1.688  H91   DYM  28  
DYM  H92   H92   H  0  1  N  N  N  81.103  26.889  28.532  -4.799   1.548   0.288  H92   DYM  29  
DYM  H111  H111  H  0  0  N  N  N  77.337  29.572  33.485   0.046  -4.888   0.313  H111  DYM  30  
DYM  H112  H112  H  0  0  N  N  N  75.760  29.846  32.670   1.615  -5.430  -0.329  H112  DYM  31  
DYM  H113  H113  H  0  0  N  N  N  76.573  28.249  32.540   1.498  -4.820   1.340  H113  DYM  32  
DYM  HN5   HN5   H  0  1  N  N  N  75.970  29.143  30.224   0.341  -2.387   1.274  HN5   DYM  33  
DYM  HO4   HO4   H  0  1  N  N  N  75.894  31.868  29.843   4.454  -0.822   0.221  HO4   DYM  34  
DYM  HO8   HO8   H  0  1  N  N  N  80.348  24.736  29.822  -3.601   0.864  -1.731  HO8   DYM  35  
DYM  HO9   HO9   H  0  1  N  N  N  82.921  25.649  28.307  -6.821   0.300   0.534  HO9   DYM  36  
DYM  HO1B  HO1B  H  0  0  N  N  N  78.137  31.354  23.104   0.960   5.034  -0.517  HO1B  DYM  37  
#   #
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
DYM  C1   C2    SING  N  N   1  
DYM  C1   O1A   DOUB  N  N   2  
DYM  C1   O1B   SING  N  N   3  
DYM  C2   C3    DOUB  N  N   4  
DYM  C2   O6    SING  N  N   5  
DYM  C3   C4    SING  N  N   6  
DYM  C3   H3    SING  N  N   7  
DYM  C4   C5    SING  N  N   8  
DYM  C4   O4    SING  N  N   9  
DYM  C4   H4    SING  N  N  10  
DYM  C5   C6    SING  N  N  11  
DYM  C5   N5    SING  N  N  12  
DYM  C5   H5    SING  N  N  13  
DYM  C6   O6    SING  N  N  14  
DYM  C6   O7    SING  N  N  15  
DYM  C6   H6    SING  N  N  16  
DYM  C7   C8    SING  N  N  17  
DYM  C7   O7    SING  N  N  18  
DYM  C7   H71   SING  N  N  19  
DYM  C7   H72   SING  N  N  20  
DYM  C8   C9    SING  N  N  21  
DYM  C8   O8    SING  N  N  22  
DYM  C8   H8    SING  N  N  23  
DYM  C9   O9    SING  N  N  24  
DYM  C9   H91   SING  N  N  25  
DYM  C9   H92   SING  N  N  26  
DYM  C10  C11   SING  N  N  27  
DYM  C10  N5    SING  N  N  28  
DYM  C10  O10   DOUB  N  N  29  
DYM  C11  H111  SING  N  N  30  
DYM  C11  H112  SING  N  N  31  
DYM  C11  H113  SING  N  N  32  
DYM  N5   HN5   SING  N  N  33  
DYM  O4   HO4   SING  N  N  34  
DYM  O8   HO8   SING  N  N  35  
DYM  O9   HO9   SING  N  N  36  
DYM  O1B  HO1B  SING  N  N  37  
#   #
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
DYM  SMILES            ACDLabs               12.01  "C(C1=CC(C(C(O1)OCC(CO)O)NC(C)=O)O)(=O)O"  
DYM  InChI             InChI                 1.03   "InChI=1S/C11H17NO8/c1-5(14)12-9-7(16)2-8(10(17)18)20-11(9)19-4-6(15)3-13/h2,6-7,9,11,13,15-16H,3-4H2,1H3,(H,12,14)(H,17,18)/t6-,7+,9-,11-/m1/s1"  
DYM  InChIKey          InChI                 1.03   HEEZEJCEFZJVGN-YRCORFKGSA-N  
DYM  SMILES_CANONICAL  CACTVS                3.385  "CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1OC[C@H](O)CO)C(O)=O"  
DYM  SMILES            CACTVS                3.385  "CC(=O)N[CH]1[CH](O)C=C(O[CH]1OC[CH](O)CO)C(O)=O"  
DYM  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC(=O)N[C@@H]1[C@H](C=C(O[C@H]1OC[C@@H](CO)O)C(=O)O)O"  
DYM  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(=O)NC1C(C=C(OC1OCC(CO)O)C(=O)O)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
DYM  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R)-2,3-dihydroxypropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid"  
DYM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  
;(2~{R},3~{R},4~{S})-3-acetamido-2-[(2~{R})-2,3-bis(oxidanyl)propoxy]-4-oxidanyl-3,4-dihydro-2~{H}-pyran-6-carboxylic
acid
;
  
#   #
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
DYM  "CARBOHYDRATE ISOMER"                  L             PDB  ?  
DYM  "CARBOHYDRATE RING"                    dihydropyran  PDB  ?  
DYM  "CARBOHYDRATE ANOMER"                  alpha         PDB  ?  
DYM  "CARBOHYDRATE PRIMARY CARBONYL GROUP"  ketose        PDB  ?  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DYM  "Create component"          2005-11-28  RCSB  
DYM  "Modify descriptor"         2011-06-04  RCSB  
DYM  "Other modification"        2020-04-11  RCSB  
DYM  "Other modification"        2020-07-03  RCSB  
DYM  "Modify name"               2020-07-17  RCSB  
DYM  "Modify synonyms"           2020-07-17  RCSB  
DYM  "Modify component atom id"  2020-07-17  RCSB  
##
