data_3KA
#

_chem_comp.id                                   3KA
_chem_comp.name                                 "1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H13 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "L-2'-DEOXYURIDINE-5'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-09-03
_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                       308.182
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3KA
_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       4WB2
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
3KA  O4     O1   O  0  1  N  N  N  -11.640  20.119  30.744  -5.255  -2.615  -0.375  O4     3KA   1  
3KA  C4     C1   C  0  1  N  N  N  -11.260  18.934  30.884  -4.371  -1.803  -0.172  C4     3KA   2  
3KA  N3     N1   N  0  1  N  N  N   -9.965  18.681  31.103  -4.663  -0.491  -0.068  N3     3KA   3  
3KA  C2     C2   C  0  1  N  N  N   -9.528  17.429  31.270  -3.684   0.406   0.155  C2     3KA   4  
3KA  O2     O2   O  0  1  N  N  N   -8.312  17.202  31.468  -3.963   1.586   0.247  O2     3KA   5  
3KA  C5     C3   C  0  1  N  N  N  -12.184  17.894  30.826  -3.027  -2.228  -0.038  C5     3KA   6  
3KA  C6     C4   C  0  1  N  N  N  -11.740  16.589  30.996  -2.066  -1.307   0.187  C6     3KA   7  
3KA  N1     N2   N  0  1  N  N  N  -10.437  16.358  31.200  -2.403   0.016   0.280  N1     3KA   8  
3KA  "C1'"  C5   C  0  1  N  N  S   -9.956  14.999  31.438  -1.360   1.015   0.523  "C1'"  3KA   9  
3KA  "O4'"  O3   O  0  1  N  N  N  -10.851  14.465  32.426  -0.062   0.388   0.596  "O4'"  3KA  10  
3KA  "C2'"  C6   C  0  1  N  N  N  -10.013  14.007  30.287  -1.231   1.975  -0.688  "C2'"  3KA  11  
3KA  "C3'"  C7   C  0  1  N  N  R  -10.141  12.714  31.068   0.227   2.477  -0.549  "C3'"  3KA  12  
3KA  "O3'"  O4   O  0  1  N  N  N   -8.892  12.437  31.707   0.258   3.749   0.101  "O3'"  3KA  13  
3KA  "C4'"  C8   C  0  1  N  N  S  -11.091  13.073  32.193   0.913   1.408   0.324  "C4'"  3KA  14  
3KA  "C5'"  C9   C  0  1  N  N  N  -12.554  12.837  31.817   2.101   0.806  -0.429  "C5'"  3KA  15  
3KA  "O5'"  O5   O  0  1  N  N  N  -13.295  12.850  33.026   2.800  -0.098   0.429  "O5'"  3KA  16  
3KA  P      P1   P  0  1  N  N  N  -14.862  12.518  33.110   4.108  -0.915  -0.036  P      3KA  17  
3KA  OP1    O6   O  0  1  N  N  N  -15.257  11.478  32.087   3.799  -1.682  -1.263  OP1    3KA  18  
3KA  OP2    O7   O  0  1  N  N  N  -15.169  12.266  34.568   5.307   0.117  -0.335  OP2    3KA  19  
3KA  O1     O8   O  0  1  N  Y  N  -15.553  13.915  32.695   4.551  -1.929   1.133  O1     3KA  20  
3KA  H1     H1   H  0  1  N  N  N   -9.314  19.439  31.142  -5.581  -0.192  -0.156  H1     3KA  21  
3KA  H2     H2   H  0  1  N  N  N  -13.230  18.099  30.651  -2.775  -3.276  -0.113  H2     3KA  22  
3KA  H3     H3   H  0  1  N  N  N  -12.440  15.767  30.964  -1.035  -1.613   0.292  H3     3KA  23  
3KA  H4     H4   H  0  1  N  N  N   -8.930  15.031  31.833  -1.569   1.572   1.436  H4     3KA  24  
3KA  H5     H5   H  0  1  N  N  N   -9.095  14.030  29.681  -1.370   1.438  -1.626  H5     3KA  25  
3KA  H6     H6   H  0  1  N  N  N  -10.885  14.182  29.639  -1.936   2.801  -0.606  H6     3KA  26  
3KA  H7     H7   H  0  1  N  N  N  -10.517  11.886  30.449   0.704   2.538  -1.527  H7     3KA  27  
3KA  H8     H8   H  0  1  N  N  N   -8.961  11.628  32.200  -0.211   4.447  -0.377  H8     3KA  28  
3KA  H9     H9   H  0  1  N  N  N  -10.844  12.480  33.086   1.253   1.855   1.259  H9     3KA  29  
3KA  H10    H10  H  0  1  N  N  N  -12.907  13.636  31.148   1.740   0.269  -1.306  H10    3KA  30  
3KA  H11    H11  H  0  1  N  N  N  -12.664  11.864  31.316   2.775   1.603  -0.743  H11    3KA  31  
3KA  H12    H12  H  0  1  N  N  N  -15.602  11.425  34.660   5.562   0.655   0.427  H12    3KA  32  
3KA  H13    H13  H  0  1  N  N  N  -16.060  13.794  31.901   5.334  -2.455   0.922  H13    3KA  33  
#   #
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
3KA  "C2'"  "C3'"  SING  N  N   1  
3KA  "C2'"  "C1'"  SING  N  N   2  
3KA  O4     C4     DOUB  N  N   3  
3KA  C5     C4     SING  N  N   4  
3KA  C5     C6     DOUB  N  N   5  
3KA  C4     N3     SING  N  N   6  
3KA  C6     N1     SING  N  N   7  
3KA  "C3'"  "O3'"  SING  N  N   8  
3KA  "C3'"  "C4'"  SING  N  N   9  
3KA  N3     C2     SING  N  N  10  
3KA  N1     C2     SING  N  N  11  
3KA  N1     "C1'"  SING  N  N  12  
3KA  C2     O2     DOUB  N  N  13  
3KA  "C1'"  "O4'"  SING  N  N  14  
3KA  "C5'"  "C4'"  SING  N  N  15  
3KA  "C5'"  "O5'"  SING  N  N  16  
3KA  OP1    P      DOUB  N  N  17  
3KA  "C4'"  "O4'"  SING  N  N  18  
3KA  "O5'"  P      SING  N  N  19  
3KA  P      OP2    SING  N  N  20  
3KA  P      O1     SING  N  N  21  
3KA  N3     H1     SING  N  N  22  
3KA  C5     H2     SING  N  N  23  
3KA  C6     H3     SING  N  N  24  
3KA  "C1'"  H4     SING  N  N  25  
3KA  "C2'"  H5     SING  N  N  26  
3KA  "C2'"  H6     SING  N  N  27  
3KA  "C3'"  H7     SING  N  N  28  
3KA  "O3'"  H8     SING  N  N  29  
3KA  "C4'"  H9     SING  N  N  30  
3KA  "C5'"  H10    SING  N  N  31  
3KA  "C5'"  H11    SING  N  N  32  
3KA  OP2    H12    SING  N  N  33  
3KA  O1     H13    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
3KA  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O"  
3KA  InChI             InChI                 1.03   "InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m1/s1"  
3KA  InChIKey          InChI                 1.03   JSRLJPSBLDHEIO-CHKWXVPMSA-N  
3KA  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1C[C@H](O[C@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"  
3KA  SMILES            CACTVS                3.385  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"  
3KA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C1[C@H]([C@@H](O[C@@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O"  
3KA  SMILES            "OpenEye OEToolkits"  1.9.2  "C1C(C(OC1N2C=CC(=O)NC2=O)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
3KA  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione"  
3KA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "[(2S,3R,5S)-5-[2,4-bis(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
3KA  "Create component"   2014-09-03  EBI   
3KA  "Modify descriptor"  2014-09-05  RCSB  
3KA  "Initial release"    2015-05-06  RCSB  
3KA  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3KA
_pdbx_chem_comp_synonyms.name        "L-2'-DEOXYURIDINE-5'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
