data_0KZ
#

_chem_comp.id                                   0KZ
_chem_comp.name                                 
;[(1R,2S,4S,5S)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen
phosphate
;

_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C12 H17 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-exo-methanocarba-thymidine monophosphate; North-methanocarba-thymidine monophosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-02-07
_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                       332.246
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    0KZ
_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       4DKZ
_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
0KZ  C2     C2     C  0  1  N  N  N  -3.278  15.405  5.776  -2.486  -0.949   0.275  C2     NC1   1  
0KZ  N3     N3     N  0  1  N  N  N  -3.434  15.224  7.174  -3.575  -1.740   0.290  N3     NC1   2  
0KZ  C4     C4     C  0  1  N  N  N  -4.266  14.290  7.829  -4.796  -1.220   0.055  C4     NC1   3  
0KZ  C5     C5     C  0  1  N  N  N  -5.051  13.411  6.960  -4.922   0.165  -0.208  C5     NC1   4  
0KZ  C6     C6     C  0  1  N  N  N  -4.916  13.572  5.635  -3.813   0.936  -0.218  C6     NC1   5  
0KZ  C7     C7     C  0  1  N  N  N  -5.970  12.372  7.517  -6.275   0.772  -0.475  C7     NC1   6  
0KZ  P      P      P  0  1  N  N  N  -8.083  10.810  3.687   4.623  -0.694   0.007  P      NC1   7  
0KZ  OP1    OP1    O  0  1  N  N  N  -8.301   9.909  2.533   4.311  -2.050   0.512  OP1    NC1   8  
0KZ  OP2    OP2    O  0  1  N  N  N  -7.907  10.309  5.067   5.202  -0.799  -1.492  OP2    NC1   9  
0KZ  "O5'"  "O5'"  O  0  1  N  N  N  -6.884  11.846  3.440   3.283   0.199   0.004  "O5'"  NC1  10  
0KZ  "C5'"  "C5'"  C  0  1  N  N  N  -6.578  12.348  2.119   2.085  -0.198  -0.665  "C5'"  NC1  11  
0KZ  "C4'"  "C4'"  C  0  1  N  N  R  -5.406  13.382  1.858   1.012   0.874  -0.469  "C4'"  NC1  12  
0KZ  "C6'"  "C6'"  C  0  1  N  N  S  -5.488  14.526  2.904  -0.399   0.713  -1.062  "C6'"  NC1  13  
0KZ  "C7'"  "C7'"  C  0  1  N  N  N  -5.333  14.811  1.374   0.598   1.746  -1.656  "C7'"  NC1  14  
0KZ  "C1'"  "C1'"  C  0  1  N  N  S  -4.006  14.616  3.441  -1.388   1.204   0.015  "C1'"  NC1  15  
0KZ  N1     N1     N  0  1  N  N  N  -4.076  14.520  4.981  -2.592   0.368   0.026  N1     NC1  16  
0KZ  O2     O2     O  0  1  N  N  N  -2.525  16.250  5.325  -1.391  -1.432   0.493  O2     NC1  17  
0KZ  O4     O4     O  0  1  N  N  N  -4.290  14.260  9.055  -5.782  -1.935   0.069  O4     NC1  18  
0KZ  "C2'"  "C2'"  C  0  1  N  N  N  -3.246  13.295  3.054  -0.610   1.050   1.345  "C2'"  NC1  19  
0KZ  "C3'"  "C3'"  C  0  1  N  N  S  -4.269  12.396  2.332   0.830   1.445   0.953  "C3'"  NC1  20  
0KZ  "O3'"  "O3'"  O  0  1  N  N  N  -3.819  11.755  1.120   0.951   2.869   0.940  "O3'"  NC1  21  
0KZ  H1     H1     H  0  1  N  N  N  -2.894  15.826  7.762  -3.480  -2.689   0.471  H1     NC1  22  
0KZ  H2     H2     H  0  1  N  N  N  -5.500  12.920  5.003  -3.889   1.994  -0.417  H2     NC1  23  
0KZ  H3     H3     H  0  1  N  N  N  -5.936  12.403  8.616  -7.038  -0.005  -0.424  H3     NC1  24  
0KZ  H4     H4     H  0  1  N  N  N  -6.997  12.570  7.176  -6.485   1.536   0.274  H4     NC1  25  
0KZ  H5     H5     H  0  1  N  N  N  -5.654  11.378  7.168  -6.282   1.224  -1.467  H5     NC1  26  
0KZ  H7     H7     H  0  1  N  N  N  -7.958   9.360  5.069   5.428   0.054  -1.887  H7     NC1  27  
0KZ  H8     H8     H  0  1  N  N  N  -7.498  12.828  1.753   2.286  -0.320  -1.730  H8     NC1  28  
0KZ  H9     H9     H  0  1  N  N  N  -6.353  11.467  1.501   1.734  -1.143  -0.251  H9     NC1  29  
0KZ  H10    H10    H  0  1  N  N  N  -6.379  14.773  3.499  -0.677  -0.175  -1.630  H10    NC1  30  
0KZ  H11    H11    H  0  1  N  N  N  -4.385  15.210  0.984   0.401   2.800  -1.461  H11    NC1  31  
0KZ  H12    H12    H  0  1  N  N  N  -6.172  15.242  0.809   1.048   1.524  -2.624  H12    NC1  32  
0KZ  H13    H13    H  0  1  N  N  N  -3.486  15.520  3.090  -1.652   2.248  -0.157  H13    NC1  33  
0KZ  H14    H14    H  0  1  N  N  N  -2.871  12.793  3.958  -1.006   1.724   2.105  H14    NC1  34  
0KZ  H15    H15    H  0  1  N  N  N  -2.403  13.524  2.386  -0.640   0.018   1.693  H15    NC1  35  
0KZ  H16    H16    H  0  1  N  N  N  -4.690  11.665  3.038   1.556   1.005   1.636  H16    NC1  36  
0KZ  H17    H17    H  0  1  N  N  N  -3.126  11.139  1.326   0.845   3.280   1.808  H17    NC1  37  
0KZ  OP3    OP3    O  0  1  N  Y  N       ?       ?      ?   5.724  -0.007   0.960  OP3    NC1  38  
0KZ  H19    H19    H  0  1  N  Y  N       ?       ?      ?   6.559  -0.492   1.010  H19    NC1  39  
#   #
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
0KZ  "O3'"  "C3'"  SING  N  N   1  
0KZ  "C7'"  "C4'"  SING  N  N   2  
0KZ  "C7'"  "C6'"  SING  N  N   3  
0KZ  "C4'"  "C5'"  SING  N  N   4  
0KZ  "C4'"  "C3'"  SING  N  N   5  
0KZ  "C4'"  "C6'"  SING  N  N   6  
0KZ  "C5'"  "O5'"  SING  N  N   7  
0KZ  "C3'"  "C2'"  SING  N  N   8  
0KZ  OP1    P      DOUB  N  N   9  
0KZ  "C6'"  "C1'"  SING  N  N  10  
0KZ  "C2'"  "C1'"  SING  N  N  11  
0KZ  "O5'"  P      SING  N  N  12  
0KZ  "C1'"  N1     SING  N  N  13  
0KZ  P      OP2    SING  N  N  14  
0KZ  N1     C6     SING  N  N  15  
0KZ  N1     C2     SING  N  N  16  
0KZ  O2     C2     DOUB  N  N  17  
0KZ  C6     C5     DOUB  N  N  18  
0KZ  C2     N3     SING  N  N  19  
0KZ  C5     C7     SING  N  N  20  
0KZ  C5     C4     SING  N  N  21  
0KZ  N3     C4     SING  N  N  22  
0KZ  C4     O4     DOUB  N  N  23  
0KZ  N3     H1     SING  N  N  24  
0KZ  C6     H2     SING  N  N  25  
0KZ  C7     H3     SING  N  N  26  
0KZ  C7     H4     SING  N  N  27  
0KZ  C7     H5     SING  N  N  28  
0KZ  OP2    H7     SING  N  N  29  
0KZ  "C5'"  H8     SING  N  N  30  
0KZ  "C5'"  H9     SING  N  N  31  
0KZ  "C6'"  H10    SING  N  N  32  
0KZ  "C7'"  H11    SING  N  N  33  
0KZ  "C7'"  H12    SING  N  N  34  
0KZ  "C1'"  H13    SING  N  N  35  
0KZ  "C2'"  H14    SING  N  N  36  
0KZ  "C2'"  H15    SING  N  N  37  
0KZ  "C3'"  H16    SING  N  N  38  
0KZ  "O3'"  H17    SING  N  N  39  
0KZ  P      OP3    SING  N  N  40  
0KZ  OP3    H19    SING  N  N  41  
#   #
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
0KZ  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC32C(C(N1C=C(C(=O)NC1=O)C)CC2O)C3"  
0KZ  InChI             InChI                 1.03   "InChI=1S/C12H17N2O7P/c1-6-4-14(11(17)13-10(6)16)8-2-9(15)12(3-7(8)12)5-21-22(18,19)20/h4,7-9,15H,2-3,5H2,1H3,(H,13,16,17)(H2,18,19,20)/t7-,8+,9+,12+/m1/s1"  
0KZ  InChIKey          InChI                 1.03   UGXPFKYDADDXLN-ARHDFHRDSA-N  
0KZ  SMILES_CANONICAL  CACTVS                3.370  "CC1=CN([C@H]2C[C@H](O)[C@]3(CO[P](O)(O)=O)C[C@H]23)C(=O)NC1=O"  
0KZ  SMILES            CACTVS                3.370  "CC1=CN([CH]2C[CH](O)[C]3(CO[P](O)(O)=O)C[CH]23)C(=O)NC1=O"  
0KZ  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H](C3([C@@H]2C3)COP(=O)(O)O)O"  
0KZ  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)C2CC(C3(C2C3)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
0KZ  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(1R,2S,4S,5S)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate"  
0KZ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(1S,2S,4S)-2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-bicyclo[3.1.0]hexanyl]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
0KZ  "Create component"  2012-02-07  RCSB  
0KZ  "Modify synonyms"   2020-06-05  PDBE  
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  0KZ  "2'-exo-methanocarba-thymidine monophosphate"  ?  ?  
2  0KZ  "North-methanocarba-thymidine monophosphate"   ?  ?  
##
