data_4SC
#

_chem_comp.id                                   4SC
_chem_comp.name                                 "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O6 P S"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_chem_comp.pdbx_modified_date                   2022-04-07
_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                       337.289
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    4SC
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6MHT
_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
4SC  P       P       P  0  1  N  N  N  -19.306  45.420  87.739  -3.784   1.166  -0.065  P       4SC   1  
4SC  OP1     O1P     O  0  1  N  N  N  -19.710  45.872  86.370  -4.967   0.544   0.570  OP1     4SC   2  
4SC  OP2     O2P     O  0  1  N  N  N  -17.881  45.200  87.986  -3.352   2.473   0.771  OP2     4SC   3  
4SC  "O5'"   "O5'"   O  0  1  N  N  N  -20.057  43.953  87.967  -2.566   0.113  -0.080  "O5'"   4SC   4  
4SC  "C5'"   "C5'"   C  0  1  N  N  N  -19.584  42.997  88.988  -2.672  -1.191  -0.654  "C5'"   4SC   5  
4SC  "C4'"   "C4'"   C  0  1  N  N  R  -20.227  41.613  88.748  -1.340  -1.927  -0.499  "C4'"   4SC   6  
4SC  "S4'"   "S4'"   S  0  1  N  N  N  -19.615  41.206  87.075  -0.001  -1.078  -1.434  "S4'"   4SC   7  
4SC  "C3'"   "C3'"   C  0  1  N  N  S  -19.735  40.545  89.724  -0.803  -1.812   0.952  "C3'"   4SC   8  
4SC  "O3'"   "O3'"   O  0  1  N  N  N  -20.543  40.545  91.028  -1.461  -2.769   1.785  "O3'"   4SC   9  
4SC  "C2'"   "C2'"   C  0  1  N  N  N  -20.000  39.193  88.937   0.702  -2.085   0.948  "C2'"   4SC  10  
4SC  "C1'"   "C1'"   C  0  1  N  N  R  -19.633  39.423  87.466   1.372  -1.668  -0.371  "C1'"   4SC  11  
4SC  N1      N1      N  0  1  N  N  N  -18.565  38.656  86.776   2.333  -0.587  -0.135  N1      4SC  12  
4SC  C2      C2      C  0  1  N  N  N  -18.515  38.779  85.376   1.949   0.516   0.534  C2      4SC  13  
4SC  O2      O2      O  0  1  N  N  N  -19.412  39.394  84.818   0.801   0.604   0.936  O2      4SC  14  
4SC  N3      N3      N  0  1  N  N  N  -17.482  38.177  84.665   2.802   1.513   0.763  N3      4SC  15  
4SC  C4      C4      C  0  1  N  N  N  -16.486  37.441  85.286   4.056   1.442   0.336  C4      4SC  16  
4SC  N4      N4      N  0  1  N  N  N  -15.388  36.985  84.562   4.929   2.478   0.578  N4      4SC  17  
4SC  C5      C5      C  0  1  N  N  N  -16.569  37.288  86.760   4.490   0.300  -0.368  C5      4SC  18  
4SC  C6      C6      C  0  1  N  N  N  -17.601  37.907  87.431   3.612  -0.707  -0.588  C6      4SC  19  
4SC  C5M     C5M     C  0  1  N  N  N  -16.750  35.700  86.690   5.910   0.199  -0.863  C5M     4SC  20  
4SC  "H5'"   "H5'"   H  0  1  N  N  N  -18.490  42.907  88.925  -3.457  -1.750  -0.143  "H5'"   4SC  21  
4SC  "H5''"  "H5''"  H  0  0  N  N  N  -19.865  43.362  89.987  -2.919  -1.104  -1.712  "H5''"  4SC  22  
4SC  "H4'"   "H4'"   H  0  1  N  N  N  -21.325  41.670  88.712  -1.431  -2.969  -0.803  "H4'"   4SC  23  
4SC  "H3'"   "H3'"   H  0  1  N  N  N  -18.660  40.662  89.928  -0.988  -0.807   1.332  "H3'"   4SC  24  
4SC  "HO3'"  "HO3'"  H  0  0  N  Y  N  -20.209  39.870  91.608  -1.173  -2.752   2.707  "HO3'"  4SC  25  
4SC  "H2'"   "H2'"   H  0  1  N  N  N  -19.377  38.389  89.356   1.163  -1.533   1.768  "H2'"   4SC  26  
4SC  "H2''"  "H2''"  H  0  0  N  N  N  -21.061  38.915  89.018   0.868  -3.151   1.107  "H2''"  4SC  27  
4SC  "H1'"   "H1'"   H  0  1  N  N  N  -20.546  39.109  86.938   1.867  -2.523  -0.831  "H1'"   4SC  28  
4SC  HN41    HN41    H  0  0  N  N  N  -15.314  37.188  83.586   4.627   3.262   1.063  HN41    4SC  29  
4SC  HN42    HN42    H  0  0  N  N  N  -14.674  36.454  85.018   5.845   2.424   0.265  HN42    4SC  30  
4SC  H61     H61     H  0  1  N  N  N  -17.660  37.805  88.505   3.922  -1.595  -1.120  H61     4SC  31  
4SC  H71     H71     H  0  1  N  N  N  -16.842  35.296  87.709   6.456   1.101  -0.585  H71     4SC  32  
4SC  H72     H72     H  0  1  N  N  N  -17.658  35.459  86.117   6.391  -0.669  -0.413  H72     4SC  33  
4SC  H73     H73     H  0  1  N  N  N  -15.875  35.253  86.196   5.910   0.094  -1.947  H73     4SC  34  
4SC  OP3     OP3     O  0  1  N  Y  N        ?       ?       ?  -4.146   1.590  -1.575  OP3     4SC  35  
4SC  HOP2    H1      H  0  0  N  N  N  -17.389  45.387  87.195  -4.039   3.152   0.821  HOP2    4SC  36  
4SC  HOP3    H2      H  0  0  N  Y  N        ?       ?       ?  -3.415   2.006  -2.053  HOP3    4SC  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
4SC  P      OP1     DOUB  N  N   1  
4SC  P      OP2     SING  N  N   2  
4SC  P      "O5'"   SING  N  N   3  
4SC  "O5'"  "C5'"   SING  N  N   4  
4SC  "C5'"  "C4'"   SING  N  N   5  
4SC  "C5'"  "H5'"   SING  N  N   6  
4SC  "C5'"  "H5''"  SING  N  N   7  
4SC  "C4'"  "S4'"   SING  N  N   8  
4SC  "C4'"  "C3'"   SING  N  N   9  
4SC  "C4'"  "H4'"   SING  N  N  10  
4SC  "S4'"  "C1'"   SING  N  N  11  
4SC  "C3'"  "O3'"   SING  N  N  12  
4SC  "C3'"  "C2'"   SING  N  N  13  
4SC  "C3'"  "H3'"   SING  N  N  14  
4SC  "O3'"  "HO3'"  SING  N  N  15  
4SC  "C2'"  "C1'"   SING  N  N  16  
4SC  "C2'"  "H2'"   SING  N  N  17  
4SC  "C2'"  "H2''"  SING  N  N  18  
4SC  "C1'"  N1      SING  N  N  19  
4SC  "C1'"  "H1'"   SING  N  N  20  
4SC  N1     C2      SING  N  N  21  
4SC  N1     C6      SING  N  N  22  
4SC  C2     O2      DOUB  N  N  23  
4SC  C2     N3      SING  N  N  24  
4SC  N3     C4      DOUB  N  N  25  
4SC  C4     N4      SING  N  N  26  
4SC  C4     C5      SING  N  N  27  
4SC  N4     HN41    SING  N  N  28  
4SC  N4     HN42    SING  N  N  29  
4SC  C5     C6      DOUB  N  N  30  
4SC  C5     C5M     SING  N  N  31  
4SC  C6     H61     SING  N  N  32  
4SC  C5M    H71     SING  N  N  33  
4SC  C5M    H72     SING  N  N  34  
4SC  C5M    H73     SING  N  N  35  
4SC  P      OP3     SING  N  N  36  
4SC  OP2    HOP2    SING  N  N  37  
4SC  OP3    HOP3    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
4SC  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC1SC(CC1O)N1C=C(C)C(N)=NC1=O"  
4SC  InChI             InChI                 1.03   "InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(21-8)4-19-20(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1"  
4SC  InChIKey          InChI                 1.03   GBRJOHLRKRNNCY-XLPZGREQSA-N  
4SC  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)S2)C(=O)N=C1N"  
4SC  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)S2)C(=O)N=C1N"  
4SC  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](S2)COP(=O)(O)O)O"  
4SC  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)C2CC(C(S2)COP(=O)(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
4SC  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)"  
4SC  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-thiolan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
4SC  "Create component"    1999-07-08  RCSB  
4SC  "Modify descriptor"   2011-06-04  RCSB  
4SC  "Other modification"  2022-04-07  RCSB  
##
