data_4U3
#

_chem_comp.id                                   4U3
_chem_comp.name                                 "5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H13 Cl N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        "5-Chloro-5'-deoxycytidine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-05-27
_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                       341.642
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    4U3
_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       5BOM
_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
4U3  C2      C1   C   0  1  N  N  N  -1.903  -11.576  16.246  -1.970   0.118  -1.148  C2      4U3   1  
4U3  N3      N1   N   0  1  N  N  N  -0.657  -10.908  16.438  -3.015   0.815  -1.591  N3      4U3   2  
4U3  C4      C2   C   0  1  N  N  N  -0.326  -10.346  17.712  -4.080   1.001  -0.823  C4      4U3   3  
4U3  C5      C3   C   0  1  N  N  N  -1.256  -10.465  18.791  -4.105   0.455   0.478  C5      4U3   4  
4U3  C6      C4   C   0  1  N  N  N  -2.507  -11.119  18.596  -3.035  -0.252   0.914  C6      4U3   5  
4U3  CL5     CL1  CL  0  0  N  N  N  -0.840   -9.770  20.308  -5.487   0.685   1.503  CL5     4U3   6  
4U3  P       P1   P   0  1  N  N  N  -5.308   -9.340  20.599   4.589   1.102   0.201  P       4U3   7  
4U3  OP1     O1   O   0  1  N  N  N  -4.315  -10.191  21.461   5.707   0.175  -0.082  OP1     4U3   8  
4U3  OP2     O2   O   0  1  N  N  N  -4.763   -7.975  20.165   4.296   2.003  -1.101  OP2     4U3   9  
4U3  "C5'"   C5   C   0  1  N  N  N  -6.506  -11.155  19.197   2.730  -0.757  -0.272  "C5'"   4U3  10  
4U3  "O5'"   O3   O   0  1  N  N  N  -5.662  -10.076  19.298   3.272   0.257   0.577  "O5'"   4U3  11  
4U3  "C4'"   C6   C   0  1  N  N  R  -6.259  -11.900  17.896   1.484  -1.358   0.382  "C4'"   4U3  12  
4U3  "O4'"   O4   O   0  1  N  N  N  -5.175  -11.371  17.154   0.406  -0.397   0.389  "O4'"   4U3  13  
4U3  "C3'"   C7   C   0  1  N  N  S  -5.931  -13.293  18.239   0.953  -2.541  -0.457  "C3'"   4U3  14  
4U3  "O3'"   O5   O   0  1  N  N  N  -6.592  -14.097  17.363   1.400  -3.784   0.090  "O3'"   4U3  15  
4U3  "C2'"   C8   C   0  1  N  N  N  -4.446  -13.395  18.163  -0.583  -2.420  -0.348  "C2'"   4U3  16  
4U3  "C1'"   C9   C   0  1  N  N  R  -4.140  -12.340  17.154  -0.799  -1.178   0.545  "C1'"   4U3  17  
4U3  N1      N2   N   0  1  N  N  N  -2.838  -11.678  17.326  -1.963  -0.416   0.087  N1      4U3  18  
4U3  O2      O6   O   0  1  N  N  N  -2.183  -12.103  15.000  -1.004  -0.043  -1.877  O2      4U3  19  
4U3  N4      N3   N   0  1  N  N  N   0.943   -9.679  17.885  -5.153   1.724  -1.291  N4      4U3  20  
4U3  H6      H1   H   0  1  N  N  N  -3.208  -11.192  19.414  -3.030  -0.680   1.905  H6      4U3  21  
4U3  HOP2    H3   H   0  0  N  N  N  -3.881   -7.864  20.501   3.573   2.635  -0.987  HOP2    4U3  22  
4U3  "H5''"  H4   H   0  0  N  N  N  -7.548  -10.804  19.221   2.460  -0.321  -1.234  "H5''"  4U3  23  
4U3  "H5'"   H5   H   0  1  N  N  N  -6.328  -11.835  20.043   3.473  -1.540  -0.424  "H5'"   4U3  24  
4U3  "H4'"   H6   H   0  1  N  N  N  -7.179  -11.878  17.294   1.709  -1.684   1.398  "H4'"   4U3  25  
4U3  H7      H7   H   0  1  N  N  N  -6.250  -13.495  19.272   1.271  -2.446  -1.495  H7      4U3  26  
4U3  "HO3'"  H8   H   0  0  N  N  N  -6.399  -15.006  17.560   1.095  -4.561  -0.399  "HO3'"  4U3  27  
4U3  "H2'"   H9   H   0  1  N  N  N  -4.126  -14.389  17.818  -1.025  -2.264  -1.332  "H2'"   4U3  28  
4U3  "H2''"  H10  H   0  0  N  N  N  -3.976  -13.175  19.133  -1.004  -3.309   0.123  "H2''"  4U3  29  
4U3  "H1'"   H11  H   0  1  N  N  N  -4.132  -12.828  16.168  -0.926  -1.474   1.586  "H1'"   4U3  30  
4U3  H41     H12  H   0  1  N  N  N   1.582   -9.613  17.118  -5.132   2.098  -2.185  H41     4U3  31  
4U3  H42     H13  H   0  1  N  N  N   1.183   -9.283  18.771  -5.930   1.858  -0.727  H42     4U3  32  
4U3  OP3     O3P  O   0  1  N  Y  N  -6.715   -9.185  21.367   4.984   2.057   1.436  OP3     4U3  33  
4U3  HOP3    H2   H   0  0  N  Y  N  -6.674   -9.641  22.199   5.770   2.597   1.280  HOP3    4U3  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
4U3  O2     C2      DOUB  N  N   1  
4U3  C2     N3      SING  N  N   2  
4U3  C2     N1      SING  N  N   3  
4U3  N3     C4      DOUB  N  N   4  
4U3  "C1'"  "O4'"   SING  N  N   5  
4U3  "C1'"  N1      SING  N  N   6  
4U3  "C1'"  "C2'"   SING  N  N   7  
4U3  "O4'"  "C4'"   SING  N  N   8  
4U3  N1     C6      SING  N  N   9  
4U3  "O3'"  "C3'"   SING  N  N  10  
4U3  C4     N4      SING  N  N  11  
4U3  C4     C5      SING  N  N  12  
4U3  "C4'"  "C3'"   SING  N  N  13  
4U3  "C4'"  "C5'"   SING  N  N  14  
4U3  "C2'"  "C3'"   SING  N  N  15  
4U3  C6     C5      DOUB  N  N  16  
4U3  C5     CL5     SING  N  N  17  
4U3  "C5'"  "O5'"   SING  N  N  18  
4U3  "O5'"  P       SING  N  N  19  
4U3  OP2    P       SING  N  N  20  
4U3  P      OP1     DOUB  N  N  21  
4U3  C6     H6      SING  N  N  22  
4U3  OP2    HOP2    SING  N  N  23  
4U3  "C5'"  "H5''"  SING  N  N  24  
4U3  "C5'"  "H5'"   SING  N  N  25  
4U3  "C4'"  "H4'"   SING  N  N  26  
4U3  "C3'"  H7      SING  N  N  27  
4U3  "O3'"  "HO3'"  SING  N  N  28  
4U3  "C2'"  "H2'"   SING  N  N  29  
4U3  "C2'"  "H2''"  SING  N  N  30  
4U3  "C1'"  "H1'"   SING  N  N  31  
4U3  N4     H41     SING  N  N  32  
4U3  N4     H42     SING  N  N  33  
4U3  P      OP3     SING  N  N  34  
4U3  OP3    HOP3    SING  N  N  35  
#   #
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
4U3  SMILES            ACDLabs               12.01  "C1(N=C(N)C(Cl)=CN1C2OC(COP(=O)(O)O)C(O)C2)=O"  
4U3  InChI             InChI                 1.03   "InChI=1S/C9H13ClN3O7P/c10-4-2-13(9(15)12-8(4)11)7-1-5(14)6(20-7)3-19-21(16,17)18/h2,5-7,14H,1,3H2,(H2,11,12,15)(H2,16,17,18)/t5-,6+,7+/m0/s1"  
4U3  InChIKey          InChI                 1.03   JXVVNBLPBHXIAA-RRKCRQDMSA-N  
4U3  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1Cl)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"  
4U3  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1Cl)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"  
4U3  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Cl)COP(=O)(O)O)O"  
4U3  SMILES            "OpenEye OEToolkits"  1.9.2  "C1C(C(OC1N2C=C(C(=NC2=O)N)Cl)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
4U3  "SYSTEMATIC NAME"  ACDLabs               12.01  "5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)"  
4U3  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "[(2R,3S,5R)-5-(4-azanyl-5-chloranyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-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
4U3  "Create component"  2015-05-27  RCSB  
4U3  "Initial release"   2015-08-19  RCSB  
4U3  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     4U3
_pdbx_chem_comp_synonyms.name        "5-Chloro-5'-deoxycytidine"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
