data_2WP
#

_chem_comp.id                                   2WP
_chem_comp.name                                 S-ribosylhomocysteine
_chem_comp.type                                 "D-saccharide, alpha linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C9 H17 N O6 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-03-13
_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                       267.299
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    2WP
_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       4OJT
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     2WP
_pdbx_chem_comp_synonyms.name        "(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
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
2WP  C1   C1   C  0  1  N  N  S  38.744   -4.139  31.086  -4.030   1.308  -0.462  C1   2WP   1  
2WP  O1   O1   O  0  1  N  Y  N  40.188   -4.156  30.997  -4.376   1.974   0.754  O1   2WP   2  
2WP  C2   C2   C  0  1  N  N  R  38.293   -3.673  32.510  -4.677  -0.090  -0.495  C2   2WP   3  
2WP  O2   O2   O  0  1  N  N  N  39.034   -2.598  32.979  -5.456  -0.309   0.683  O2   2WP   4  
2WP  C3   C3   C  0  1  N  N  S  38.585   -4.961  33.298  -3.475  -1.065  -0.538  C3   2WP   5  
2WP  O3   O3   O  0  1  N  N  N  39.949   -5.235  33.393  -3.703  -2.194   0.307  O3   2WP   6  
2WP  C4   C4   C  0  1  N  N  S  38.024   -6.035  32.321  -2.324  -0.185   0.015  C4   2WP   7  
2WP  O4   O4   O  0  1  N  N  N  38.206   -5.461  31.011  -2.606   1.121  -0.533  O4   2WP   8  
2WP  C5   CE   C  0  1  N  N  N  36.528   -6.279  32.591  -0.970  -0.696  -0.480  C5   2WP   9  
2WP  N    N    N  0  1  N  N  N  35.377  -11.613  31.527   4.470  -1.789   0.026  N    2WP  10  
2WP  CA   CA   C  0  1  N  N  S  36.492  -11.570  32.482   4.357  -0.395  -0.422  CA   2WP  11  
2WP  CB   CB   C  0  1  N  N  N  36.295  -10.347  33.425   3.091   0.229   0.169  CB   2WP  12  
2WP  CG   CG   C  0  1  N  N  N  36.453   -9.054  32.640   1.860  -0.479  -0.400  CG   2WP  13  
2WP  SD   SD   S  0  1  N  N  N  36.262   -7.641  33.801   0.359   0.261   0.300  SD   2WP  14  
2WP  C    C    C  0  1  N  N  N  36.529  -12.880  33.349   5.563   0.381   0.042  C    2WP  15  
2WP  O    O    O  0  1  N  N  N  35.412  -13.384  33.577   6.234  -0.036   0.956  O    2WP  16  
2WP  OXT  OXT  O  0  1  N  N  N  37.638  -13.310  33.726   5.891   1.534  -0.561  OXT  2WP  17  
2WP  H1   H1   H  0  1  N  N  N  38.304   -3.479  30.324  -4.370   1.894  -1.316  H1   2WP  18  
2WP  HO1  H2   H  0  1  N  Y  N  40.519   -3.267  31.049  -3.999   2.861   0.837  HO1  2WP  19  
2WP  H2   H3   H  0  1  N  N  N  37.212   -3.468  32.509  -5.294  -0.204  -1.386  H2   2WP  20  
2WP  HO2  H4   H  0  1  N  Y  N  38.725   -2.352  33.843  -6.190   0.312   0.790  HO2  2WP  21  
2WP  H3   H5   H  0  1  N  N  N  38.055   -4.978  34.262  -3.266  -1.381  -1.560  H3   2WP  22  
2WP  HO3  H6   H  0  1  N  Y  N  40.358   -4.610  33.980  -4.470  -2.726   0.053  HO3  2WP  23  
2WP  H4   H7   H  0  1  N  N  N  38.587   -6.973  32.433  -2.349  -0.160   1.104  H4   2WP  24  
2WP  H51  H8   H  0  1  N  N  N  36.084   -5.356  32.991  -0.861  -1.748  -0.219  H51  2WP  25  
2WP  H52  H9   H  0  1  N  N  N  36.034   -6.543  31.644  -0.912  -0.582  -1.563  H52  2WP  26  
2WP  H10  H10  H  0  1  N  N  N  35.369  -10.773  30.985   4.522  -1.843   1.033  H10  2WP  27  
2WP  H11  H11  H  0  1  N  N  N  35.488  -12.400  30.920   3.705  -2.346  -0.326  H11  2WP  28  
2WP  H13  H13  H  0  1  N  N  N  37.449  -11.466  31.950   4.303  -0.366  -1.510  H13  2WP  29  
2WP  H14  H14  H  0  1  N  N  N  35.288  -10.385  33.865   3.104   0.121   1.253  H14  2WP  30  
2WP  H15  H15  H  0  1  N  N  N  37.047  -10.380  34.227   3.053   1.288  -0.090  H15  2WP  31  
2WP  H16  H16  H  0  1  N  N  N  37.450   -9.021  32.176   1.847  -0.371  -1.484  H16  2WP  32  
2WP  H17  H17  H  0  1  N  N  N  35.682   -8.998  31.857   1.898  -1.537  -0.141  H17  2WP  33  
2WP  H18  H18  H  0  1  N  N  N  37.515  -14.105  34.231   6.673   1.996  -0.228  H18  2WP  34  
#   #
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
2WP  O1   C1   SING  N  N   1  
2WP  O4   C1   SING  N  N   2  
2WP  O4   C4   SING  N  N   3  
2WP  C1   C2   SING  N  N   4  
2WP  N    CA   SING  N  N   5  
2WP  C4   C5   SING  N  N   6  
2WP  C4   C3   SING  N  N   7  
2WP  CA   C    SING  N  N   8  
2WP  CA   CB   SING  N  N   9  
2WP  C2   O2   SING  N  N  10  
2WP  C2   C3   SING  N  N  11  
2WP  C5   SD   SING  N  N  12  
2WP  CG   CB   SING  N  N  13  
2WP  CG   SD   SING  N  N  14  
2WP  C3   O3   SING  N  N  15  
2WP  C    O    DOUB  N  N  16  
2WP  C    OXT  SING  N  N  17  
2WP  C1   H1   SING  N  N  18  
2WP  O1   HO1  SING  N  N  19  
2WP  C2   H2   SING  N  N  20  
2WP  O2   HO2  SING  N  N  21  
2WP  C3   H3   SING  N  N  22  
2WP  O3   HO3  SING  N  N  23  
2WP  C4   H4   SING  N  N  24  
2WP  C5   H51  SING  N  N  25  
2WP  C5   H52  SING  N  N  26  
2WP  N    H10  SING  N  N  27  
2WP  N    H11  SING  N  N  28  
2WP  CA   H13  SING  N  N  29  
2WP  CB   H14  SING  N  N  30  
2WP  CB   H15  SING  N  N  31  
2WP  CG   H16  SING  N  N  32  
2WP  CG   H17  SING  N  N  33  
2WP  OXT  H18  SING  N  N  34  
#   #
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
2WP  SMILES            ACDLabs               12.01  "O=C(O)C(N)CCSCC1OC(O)C(O)C1O"  
2WP  InChI             InChI                 1.03   "InChI=1S/C9H17NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3,10H2,(H,13,14)/t4-,5+,6+,7+,9-/m0/s1"  
2WP  InChIKey          InChI                 1.03   IQFWYNFDWRYSRA-LYNCRYNASA-N  
2WP  SMILES_CANONICAL  CACTVS                3.385  "N[C@@H](CCSC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O)C(O)=O"  
2WP  SMILES            CACTVS                3.385  "N[CH](CCSC[CH]1O[CH](O)[CH](O)[CH]1O)C(O)=O"  
2WP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C(CSC[C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)[C@@H](C(=O)O)N"  
2WP  SMILES            "OpenEye OEToolkits"  1.7.6  "C(CSCC1C(C(C(O1)O)O)O)C(C(=O)O)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
2WP  "SYSTEMATIC NAME"  ACDLabs               12.01  
;(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred
name)
;
  
2WP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "(2S)-2-azanyl-4-[[(2S,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic 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
2WP  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
2WP  "CARBOHYDRATE RING"                    furanose  PDB  ?  
2WP  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
2WP  "CARBOHYDRATE PRIMARY CARBONYL GROUP"  aldose    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
2WP  "Create component"          2014-03-13  RCSB  
2WP  "Initial release"           2014-03-26  RCSB  
2WP  "Other modification"        2020-07-03  RCSB  
2WP  "Modify name"               2020-07-17  RCSB  
2WP  "Modify synonyms"           2020-07-17  RCSB  
2WP  "Modify internal type"      2020-07-17  RCSB  
2WP  "Modify linking type"       2020-07-17  RCSB  
2WP  "Modify atom id"            2020-07-17  RCSB  
2WP  "Modify component atom id"  2020-07-17  RCSB  
2WP  "Modify leaving atom flag"  2020-07-17  RCSB  
##
