data_38S
#

_chem_comp.id                                   38S
_chem_comp.name                                 "1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H14 N2 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "3'-deoxy thymidine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-07-08
_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                       226.229
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    38S
_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       4QSX
_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
38S  OAC  OAC  O  0  1  N  N  N  28.418  44.278  -12.359   1.530   2.528   0.520  OAC  38S   1  
38S  CAM  CAM  C  0  1  N  N  N  27.317  44.444  -11.839   1.596   1.331   0.317  CAM  38S   2  
38S  NAI  NAI  N  0  1  N  N  N  26.326  43.547  -12.169   2.801   0.743   0.203  NAI  38S   3  
38S  CAL  CAL  C  0  1  N  N  N  25.040  43.654  -11.627   2.892  -0.583  -0.023  CAL  38S   4  
38S  OAB  OAB  O  0  1  N  N  N  24.258  42.790  -11.984   3.982  -1.116  -0.126  OAB  38S   5  
38S  CAK  CAK  C  0  1  N  N  N  24.745  44.654  -10.710   1.708  -1.351  -0.137  CAK  38S   6  
38S  CAA  CAA  C  0  1  N  N  N  23.474  44.801  -10.119   1.781  -2.835  -0.388  CAA  38S   7  
38S  CAE  CAE  C  0  1  N  N  N  25.766  45.551  -10.380   0.512  -0.735  -0.017  CAE  38S   8  
38S  NAP  NAP  N  0  1  N  N  N  27.056  45.428  -10.961   0.463   0.612   0.216  NAP  38S   9  
38S  CAO  CAO  C  0  1  N  N  R  28.112  46.396  -10.595  -0.834   1.279   0.351  CAO  38S  10  
38S  OAJ  OAJ  O  0  1  N  N  N  28.100  46.576   -9.175  -1.817   0.341   0.805  OAJ  38S  11  
38S  CAH  CAH  C  0  1  N  N  N  27.750  47.700  -11.186  -1.295   1.811  -1.023  CAH  38S  12  
38S  CAG  CAG  C  0  1  N  N  N  28.576  48.590  -10.348  -2.271   0.699  -1.496  CAG  38S  13  
38S  CAN  CAN  C  0  1  N  N  S  28.465  47.944   -8.945  -2.891   0.258  -0.146  CAN  38S  14  
38S  CAF  CAF  C  0  1  N  N  N  27.449  48.646   -8.034  -3.404  -1.181  -0.243  CAF  38S  15  
38S  OAD  OAD  O  0  1  N  N  N  26.235  48.774   -8.813  -4.016  -1.552   0.994  OAD  38S  16  
38S  H1   H1   H  0  1  N  N  N  26.529  42.805  -12.808   3.608   1.276   0.282  H1   38S  17  
38S  H2   H2   H  0  1  N  N  N  23.486  45.659   -9.431   2.825  -3.141  -0.453  H2   38S  18  
38S  H3   H3   H  0  1  N  N  N  22.722  44.971  -10.904   1.297  -3.366   0.431  H3   38S  19  
38S  H4   H4   H  0  1  N  N  N  23.221  43.887   -9.561   1.274  -3.070  -1.324  H4   38S  20  
38S  H5   H5   H  0  1  N  N  N  25.571  46.346   -9.675  -0.402  -1.305  -0.102  H5   38S  21  
38S  H6   H6   H  0  1  N  N  N  29.096  46.060  -10.954  -0.754   2.103   1.060  H6   38S  22  
38S  H7   H7   H  0  1  N  N  N  28.031  47.760  -12.248  -1.815   2.763  -0.916  H7   38S  23  
38S  H8   H8   H  0  1  N  N  N  26.677  47.915  -11.078  -0.451   1.903  -1.707  H8   38S  24  
38S  H9   H9   H  0  1  N  N  N  29.620  48.605  -10.696  -3.032   1.102  -2.164  H9   38S  25  
38S  H10  H10  H  0  1  N  N  N  28.176  49.615  -10.345  -1.732  -0.122  -1.968  H10  38S  26  
38S  H11  H11  H  0  1  N  N  N  29.454  47.990   -8.465  -3.700   0.931   0.137  H11  38S  27  
38S  H12  H12  H  0  1  N  N  N  27.263  48.043   -7.133  -4.137  -1.252  -1.047  H12  38S  28  
38S  H13  H13  H  0  1  N  N  N  27.821  49.639   -7.740  -2.570  -1.851  -0.451  H13  38S  29  
38S  H14  H14  H  0  1  N  N  N  25.568  49.206   -8.292  -4.365  -2.453   1.005  H14  38S  30  
#   #
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
38S  OAC  CAM  DOUB  N  N   1  
38S  NAI  CAM  SING  N  N   2  
38S  NAI  CAL  SING  N  N   3  
38S  OAB  CAL  DOUB  N  N   4  
38S  CAM  NAP  SING  N  N   5  
38S  CAL  CAK  SING  N  N   6  
38S  CAH  CAO  SING  N  N   7  
38S  CAH  CAG  SING  N  N   8  
38S  NAP  CAO  SING  N  N   9  
38S  NAP  CAE  SING  N  N  10  
38S  CAK  CAE  DOUB  N  N  11  
38S  CAK  CAA  SING  N  N  12  
38S  CAO  OAJ  SING  N  N  13  
38S  CAG  CAN  SING  N  N  14  
38S  OAJ  CAN  SING  N  N  15  
38S  CAN  CAF  SING  N  N  16  
38S  OAD  CAF  SING  N  N  17  
38S  NAI  H1   SING  N  N  18  
38S  CAA  H2   SING  N  N  19  
38S  CAA  H3   SING  N  N  20  
38S  CAA  H4   SING  N  N  21  
38S  CAE  H5   SING  N  N  22  
38S  CAO  H6   SING  N  N  23  
38S  CAH  H7   SING  N  N  24  
38S  CAH  H8   SING  N  N  25  
38S  CAG  H9   SING  N  N  26  
38S  CAG  H10  SING  N  N  27  
38S  CAN  H11  SING  N  N  28  
38S  CAF  H12  SING  N  N  29  
38S  CAF  H13  SING  N  N  30  
38S  OAD  H14  SING  N  N  31  
#   #
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
38S  SMILES            ACDLabs               12.01  "O=C1NC(=O)N(C=C1C)C2OC(CC2)CO"  
38S  InChI             InChI                 1.03   "InChI=1S/C10H14N2O4/c1-6-4-12(10(15)11-9(6)14)8-3-2-7(5-13)16-8/h4,7-8,13H,2-3,5H2,1H3,(H,11,14,15)/t7-,8+/m0/s1"  
38S  InChIKey          InChI                 1.03   XKKCQTLDIPIRQD-JGVFFNPUSA-N  
38S  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2CC[C@@H](CO)O2)C(=O)NC1=O"  
38S  SMILES            CACTVS                3.385  "CC1=CN([CH]2CC[CH](CO)O2)C(=O)NC1=O"  
38S  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO"  
38S  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)C2CCC(O2)CO"  
#   #
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
38S  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione"  
38S  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "1-[(2R,5S)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
38S  "Create component"  2014-07-08  RCSB  
38S  "Initial release"   2014-07-23  RCSB  
38S  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     38S
_pdbx_chem_comp_synonyms.name        "3'-deoxy thymidine"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
