data_5BT
#

_chem_comp.id                                   5BT
_chem_comp.name                                 "5-bromo-2'-deoxycytidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H12 Br N3 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "5-bromo-2'-doxy-D-cytidine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2011-01-25
_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                       306.113
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5BT
_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       3QEN
_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
5BT  N1      N1      N   0  1  N  N  N  -12.529  27.938  -22.559   0.193   0.008  -0.153  N1      5BT   1  
5BT  C2      C2      C   0  1  N  N  N  -11.129  28.115  -22.503   0.177   1.312  -0.486  C2      5BT   2  
5BT  O2      O2      O   0  1  N  N  N  -10.656  29.271  -22.553   1.229   1.887  -0.712  O2      5BT   3  
5BT  N3      N3      N   0  1  N  N  N  -10.285  27.083  -22.430  -0.969   1.984  -0.575  N3      5BT   4  
5BT  C4      C4      C   0  1  N  N  N  -10.717  25.821  -22.389  -2.128   1.384  -0.336  C4      5BT   5  
5BT  N4      N4      N   0  1  N  N  N   -9.785  24.829  -22.320  -3.305   2.089  -0.431  N4      5BT   6  
5BT  C5      C5      C   0  1  N  N  N  -12.191  25.599  -22.425  -2.146   0.018   0.017  C5      5BT   7  
5BT  BR5     BR5     BR  0  0  N  N  N  -13.040  23.890  -22.392  -3.783  -0.863   0.363  BR5     5BT   8  
5BT  C6      C6      C   0  1  N  N  N  -13.030  26.707  -22.503  -0.972  -0.652   0.103  C6      5BT   9  
5BT  "C1'"   "C1'"   C   0  1  N  N  R  -13.408  29.127  -22.580   1.469  -0.706  -0.069  "C1'"   5BT  10  
5BT  "C2'"   "C2'"   C   0  1  N  N  N  -14.185  29.460  -23.853   2.176  -0.708  -1.443  "C2'"   5BT  11  
5BT  "C3'"   "C3'"   C   0  1  N  N  S  -15.555  29.862  -23.326   3.674  -0.555  -1.095  "C3'"   5BT  12  
5BT  "O3'"   "O3'"   O   0  1  N  N  N  -15.575  31.262  -22.987   4.412  -1.691  -1.551  "O3'"   5BT  13  
5BT  "C4'"   "C4'"   C   0  1  N  N  R  -15.712  29.094  -22.032   3.695  -0.480   0.448  "C4'"   5BT  14  
5BT  "O4'"   "O4'"   O   0  1  N  N  N  -14.379  28.987  -21.519   2.378  -0.012   0.812  "O4'"   5BT  15  
5BT  "C5'"   "C5'"   C   0  1  N  N  N  -16.337  27.714  -22.270   4.761   0.511   0.918  "C5'"   5BT  16  
5BT  "O5'"   "O5'"   O   0  1  N  N  N  -17.551  27.662  -21.515   4.845   0.480   2.344  "O5'"   5BT  17  
5BT  HN4     HN4     H   0  1  N  N  N   -8.812  25.058  -22.302  -3.290   3.028  -0.674  HN4     5BT  18  
5BT  HN4A    HN4A    H   0  0  N  N  N  -10.074  23.872  -22.288  -4.151   1.648  -0.255  HN4A    5BT  19  
5BT  H6      H6      H   0  1  N  N  N  -14.101  26.566  -22.518  -0.959  -1.698   0.370  H6      5BT  20  
5BT  "H1'"   "H1'"   H   0  1  N  N  N  -12.695  29.958  -22.477   1.310  -1.727   0.278  "H1'"   5BT  21  
5BT  "H2'"   "H2'"   H   0  1  N  N  N  -13.711  30.278  -24.416   1.998  -1.649  -1.963  "H2'"   5BT  22  
5BT  "H2'A"  "H2'A"  H   0  0  N  N  N  -14.248  28.594  -24.528   1.837   0.133  -2.048  "H2'A"  5BT  23  
5BT  "H3'"   "H3'"   H   0  1  N  N  N  -16.339  29.662  -24.071   4.075   0.360  -1.530  "H3'"   5BT  24  
5BT  "HO3'"  "HO3'"  H   0  0  N  N  N  -16.436  31.497  -22.660   4.382  -1.821  -2.509  "HO3'"  5BT  25  
5BT  "H4'"   "H4'"   H   0  1  N  N  N  -16.389  29.599  -21.327   3.878  -1.466   0.873  "H4'"   5BT  26  
5BT  "H5'"   "H5'"   H   0  1  N  N  N  -16.548  27.572  -23.340   5.726   0.236   0.491  "H5'"   5BT  27  
5BT  "H5'A"  "H5'A"  H   0  0  N  N  N  -15.649  26.923  -21.938   4.493   1.516   0.591  "H5'A"  5BT  28  
5BT  "HO5'"  "HO5'"  H   0  0  N  N  N  -17.966  26.817  -21.640   5.503   1.085   2.713  "HO5'"  5BT  29  
#   #
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
5BT  "C1'"  N1      SING  N  N   1  
5BT  N1     C6      SING  N  N   2  
5BT  N1     C2      SING  N  N   3  
5BT  O2     C2      DOUB  N  N   4  
5BT  C2     N3      SING  N  N   5  
5BT  N3     C4      DOUB  N  N   6  
5BT  C5     C4      SING  N  N   7  
5BT  C4     N4      SING  N  N   8  
5BT  N4     HN4     SING  N  N   9  
5BT  N4     HN4A    SING  N  N  10  
5BT  C6     C5      DOUB  N  N  11  
5BT  C5     BR5     SING  N  N  12  
5BT  C6     H6      SING  N  N  13  
5BT  "C2'"  "C1'"   SING  N  N  14  
5BT  "C1'"  "O4'"   SING  N  N  15  
5BT  "C1'"  "H1'"   SING  N  N  16  
5BT  "C2'"  "C3'"   SING  N  N  17  
5BT  "C2'"  "H2'"   SING  N  N  18  
5BT  "C2'"  "H2'A"  SING  N  N  19  
5BT  "C3'"  "O3'"   SING  N  N  20  
5BT  "C3'"  "C4'"   SING  N  N  21  
5BT  "C3'"  "H3'"   SING  N  N  22  
5BT  "O3'"  "HO3'"  SING  N  N  23  
5BT  "C5'"  "C4'"   SING  N  N  24  
5BT  "C4'"  "O4'"   SING  N  N  25  
5BT  "C4'"  "H4'"   SING  N  N  26  
5BT  "C5'"  "O5'"   SING  N  N  27  
5BT  "C5'"  "H5'"   SING  N  N  28  
5BT  "C5'"  "H5'A"  SING  N  N  29  
5BT  "O5'"  "HO5'"  SING  N  N  30  
#   #
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
5BT  SMILES            ACDLabs               12.01  "BrC=1C(=NC(=O)N(C=1)C2OC(C(O)C2)CO)N"  
5BT  SMILES_CANONICAL  CACTVS                3.370  "NC1=NC(=O)N(C=C1Br)[C@H]2C[C@H](O)[C@@H](CO)O2"  
5BT  SMILES            CACTVS                3.370  "NC1=NC(=O)N(C=C1Br)[CH]2C[CH](O)[CH](CO)O2"  
5BT  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Br)CO)O"  
5BT  SMILES            "OpenEye OEToolkits"  1.7.0  "C1C(C(OC1N2C=C(C(=NC2=O)N)Br)CO)O"  
5BT  InChI             InChI                 1.03   "InChI=1S/C9H12BrN3O4/c10-4-2-13(9(16)12-8(4)11)7-1-5(15)6(3-14)17-7/h2,5-7,14-15H,1,3H2,(H2,11,12,16)/t5-,6+,7+/m0/s1"  
5BT  InChIKey          InChI                 1.03   KISUPFXQEHWGAR-RRKCRQDMSA-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
5BT  "SYSTEMATIC NAME"  ACDLabs               12.01  "5-bromo-2'-deoxycytidine"  
5BT  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "4-azanyl-5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5BT  "Create component"   2011-01-25  RCSB  
5BT  "Modify descriptor"  2011-06-04  RCSB  
5BT  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5BT
_pdbx_chem_comp_synonyms.name        "5-bromo-2'-doxy-D-cytidine"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
