data_9BJ
#

_chem_comp.id                                   9BJ
_chem_comp.name                                 "3',3'-cdUMP"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H24 N4 O16 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-04-17
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       614.348
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9BJ
_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       5VDS
_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
9BJ  C10  C1   C  0  1  N  N  R  -23.383   3.050  27.610  -4.914  -0.093   0.845  C10  9BJ   1  
9BJ  C13  C2   C  0  1  N  N  N  -21.400   1.644  24.530  -8.146   1.396  -0.132  C13  9BJ   2  
9BJ  C21  C3   C  0  1  N  N  R  -27.502  -1.528  25.373   2.395  -0.822   0.719  C21  9BJ   3  
9BJ  C22  C4   C  0  1  N  N  N  -28.719  -1.237  25.628   2.056  -2.233   1.206  C22  9BJ   4  
9BJ  O01  O1   O  0  1  N  N  N  -24.272  -2.466  26.300   1.168   1.700  -0.116  O01  9BJ   5  
9BJ  P02  P1   P  0  1  N  N  N  -25.392  -1.766  27.043   1.054   1.407   1.330  P02  9BJ   6  
9BJ  O03  O2   O  0  1  N  N  N  -25.202  -0.103  27.159  -0.481   1.087   1.693  O03  9BJ   7  
9BJ  C04  C5   C  0  1  N  N  N  -25.564   0.547  28.383  -1.524   1.065   0.716  C04  9BJ   8  
9BJ  C05  C6   C  0  1  N  N  R  -25.173   1.876  28.344  -2.602   0.068   1.143  C05  9BJ   9  
9BJ  C06  C7   C  0  1  N  N  S  -25.581   2.575  26.943  -2.790  -0.997   0.052  C06  9BJ  10  
9BJ  O07  O3   O  0  1  N  N  N  -27.000   3.058  26.989  -2.225  -2.241   0.468  O07  9BJ  11  
9BJ  C08  C8   C  0  1  N  N  R  -24.791   3.529  26.842  -4.315  -1.131  -0.116  C08  9BJ  12  
9BJ  O09  O4   O  0  1  N  N  N  -25.341   4.726  27.506  -4.741  -2.446   0.246  O09  9BJ  13  
9BJ  N11  N1   N  0  1  N  N  N  -22.451   2.963  26.456  -5.912   0.716   0.141  N11  9BJ  14  
9BJ  C12  C9   C  0  1  N  N  N  -22.343   1.726  25.694  -7.226   0.650   0.517  C12  9BJ  15  
9BJ  C14  C10  C  0  1  N  N  N  -20.569   2.832  24.159  -7.728   2.235  -1.193  C14  9BJ  16  
9BJ  N15  N2   N  0  1  N  N  N  -20.682   4.062  24.928  -6.423   2.273  -1.532  N15  9BJ  17  
9BJ  C16  C11  C  0  1  N  N  N  -21.621   4.141  26.082  -5.528   1.518  -0.869  C16  9BJ  18  
9BJ  O17  O5   O  0  1  N  N  N  -21.706   5.148  26.703  -4.355   1.562  -1.186  O17  9BJ  19  
9BJ  O18  O6   O  0  1  N  N  N  -19.818   2.770  23.238  -8.539   2.917  -1.793  O18  9BJ  20  
9BJ  O19  O7   O  0  1  N  N  N  -23.674   2.010  28.378  -3.852   0.743   1.307  O19  9BJ  21  
9BJ  O20  O8   O  0  1  N  N  N  -26.909  -2.246  26.539   1.969   0.133   1.693  O20  9BJ  22  
9BJ  C23  C12  C  0  1  N  N  N  -28.819   0.169  26.176   1.431  -3.031   0.061  C23  9BJ  23  
9BJ  O24  O9   O  0  1  N  N  N  -28.061   1.048  25.338   0.113  -3.443   0.431  O24  9BJ  24  
9BJ  P25  P2   P  0  1  N  N  N  -27.987   2.690  25.692  -1.194  -3.083  -0.438  P25  9BJ  25  
9BJ  O26  O10  O  0  1  N  N  N  -27.736   3.554  24.473  -0.798  -2.276  -1.614  O26  9BJ  26  
9BJ  O27  O11  O  0  1  N  N  N  -29.376   3.078  26.144  -1.900  -4.443  -0.932  O27  9BJ  27  
9BJ  O28  O12  O  0  1  N  N  N  -29.554  -1.379  24.190   3.925   1.654   1.050  O28  9BJ  28  
9BJ  C29  C13  C  0  1  N  N  R  -28.772  -1.940  23.318   4.245   0.708   0.028  C29  9BJ  29  
9BJ  N30  N3   N  0  1  N  N  N  -28.111  -1.161  22.228   5.674   0.788  -0.282  N30  9BJ  30  
9BJ  C31  C14  C  0  1  N  N  N  -27.748  -1.820  20.941   6.071   1.001  -1.550  C31  9BJ  31  
9BJ  N32  N4   N  0  1  N  N  N  -27.108  -1.026  19.850   7.378   1.079  -1.862  N32  9BJ  32  
9BJ  C33  C15  C  0  1  N  N  N  -26.839   0.394  20.035   8.315   0.943  -0.903  C33  9BJ  33  
9BJ  C34  C16  C  0  1  N  N  N  -27.207   1.061  21.323   7.912   0.719   0.436  C34  9BJ  34  
9BJ  C35  C17  C  0  1  N  N  N  -27.849   0.259  22.414   6.594   0.650   0.722  C35  9BJ  35  
9BJ  O36  O13  O  0  1  N  N  N  -26.327   1.027  19.168   9.498   1.013  -1.185  O36  9BJ  36  
9BJ  O37  O14  O  0  1  N  N  N  -27.966  -2.977  20.782   5.236   1.125  -2.425  O37  9BJ  37  
9BJ  C38  C18  C  0  1  N  N  R  -27.568  -2.485  24.129   3.906  -0.702   0.515  C38  9BJ  38  
9BJ  O39  O15  O  0  1  N  N  N  -27.814  -3.734  24.529   4.332  -1.658  -0.459  O39  9BJ  39  
9BJ  O40  O16  O  0  1  N  N  N  -25.308  -2.273  28.460   1.551   2.683   2.177  O40  9BJ  40  
9BJ  H1   H1   H  0  1  N  N  N  -23.074   3.904  28.230  -5.379  -0.598   1.691  H1   9BJ  41  
9BJ  H2   H2   H  0  1  N  N  N  -21.321   0.729  23.961  -9.187   1.349   0.151  H2   9BJ  42  
9BJ  H3   H3   H  0  1  N  N  N  -26.886  -0.653  25.118   1.884  -0.631  -0.225  H3   9BJ  43  
9BJ  H4   H4   H  0  1  N  N  N  -29.311  -1.309  24.703   2.967  -2.730   1.541  H4   9BJ  44  
9BJ  H5   H5   H  0  1  N  N  N  -29.113  -1.945  26.372   1.350  -2.171   2.034  H5   9BJ  45  
9BJ  H6   H6   H  0  1  N  N  N  -26.654   0.491  28.517  -1.963   2.059   0.631  H6   9BJ  46  
9BJ  H7   H7   H  0  1  N  N  N  -25.065   0.044  29.225  -1.113   0.765  -0.248  H7   9BJ  47  
9BJ  H8   H8   H  0  1  N  N  N  -25.619   2.456  29.165  -2.316  -0.409   2.080  H8   9BJ  48  
9BJ  H9   H9   H  0  1  N  N  N  -25.474   1.825  26.145  -2.335  -0.667  -0.882  H9   9BJ  49  
9BJ  H10  H10  H  0  1  N  N  N  -24.528   3.772  25.802  -4.604  -0.908  -1.143  H10  9BJ  50  
9BJ  H11  H11  H  0  1  N  N  N  -26.140   4.994  27.067  -5.699  -2.575   0.203  H11  9BJ  51  
9BJ  H12  H12  H  0  1  N  N  N  -22.941   0.869  25.967  -7.526   0.004   1.328  H12  9BJ  52  
9BJ  H13  H13  H  0  1  N  N  N  -20.128   4.857  24.681  -6.129   2.845  -2.258  H13  9BJ  53  
9BJ  H14  H14  H  0  1  N  N  N  -29.872   0.487  26.188   1.380  -2.407  -0.831  H14  9BJ  54  
9BJ  H15  H15  H  0  1  N  N  N  -28.416   0.196  27.199   2.042  -3.910  -0.145  H15  9BJ  55  
9BJ  H16  H16  H  0  1  N  N  N  -29.724   3.745  25.564  -1.336  -5.001  -1.485  H16  9BJ  56  
9BJ  H17  H17  H  0  1  N  N  N  -29.875  -2.036  24.797   4.405   1.515   1.878  H17  9BJ  57  
9BJ  H18  H18  H  0  1  N  N  N  -29.269  -2.806  22.857   3.666   0.932  -0.868  H18  9BJ  58  
9BJ  H19  H19  H  0  1  N  N  N  -26.863  -1.471  18.989   7.646   1.232  -2.782  H19  9BJ  59  
9BJ  H20  H20  H  0  1  N  N  N  -27.011   2.114  21.465   8.648   0.608   1.218  H20  9BJ  60  
9BJ  H21  H21  H  0  1  N  N  N  -28.119   0.737  23.344   6.267   0.483   1.738  H21  9BJ  61  
9BJ  H22  H22  H  0  1  N  N  N  -26.644  -2.390  23.539   4.417  -0.893   1.459  H22  9BJ  62  
9BJ  H23  H23  H  0  1  N  N  N  -27.853  -4.307  23.773   3.918  -1.548  -1.325  H23  9BJ  63  
9BJ  H24  H24  H  0  1  N  N  N  -24.590  -2.891  28.534   1.043   3.489   2.008  H24  9BJ  64  
#   #
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
9BJ  C10  C08  SING  N  N   1  
9BJ  C10  N11  SING  N  N   2  
9BJ  C10  O19  SING  N  N   3  
9BJ  C13  C12  DOUB  N  N   4  
9BJ  C13  C14  SING  N  N   5  
9BJ  C21  C22  SING  N  N   6  
9BJ  C21  O20  SING  N  N   7  
9BJ  C21  C38  SING  N  N   8  
9BJ  C22  C23  SING  N  N   9  
9BJ  O01  P02  DOUB  N  N  10  
9BJ  P02  O03  SING  N  N  11  
9BJ  P02  O20  SING  N  N  12  
9BJ  P02  O40  SING  N  N  13  
9BJ  O03  C04  SING  N  N  14  
9BJ  C04  C05  SING  N  N  15  
9BJ  C05  C06  SING  N  N  16  
9BJ  C05  O19  SING  N  N  17  
9BJ  C06  O07  SING  N  N  18  
9BJ  C06  C08  SING  N  N  19  
9BJ  O07  P25  SING  N  N  20  
9BJ  C08  O09  SING  N  N  21  
9BJ  N11  C12  SING  N  N  22  
9BJ  N11  C16  SING  N  N  23  
9BJ  C14  N15  SING  N  N  24  
9BJ  C14  O18  DOUB  N  N  25  
9BJ  N15  C16  SING  N  N  26  
9BJ  C16  O17  DOUB  N  N  27  
9BJ  C23  O24  SING  N  N  28  
9BJ  O24  P25  SING  N  N  29  
9BJ  P25  O26  DOUB  N  N  30  
9BJ  P25  O27  SING  N  N  31  
9BJ  O28  C29  SING  N  N  32  
9BJ  C29  N30  SING  N  N  33  
9BJ  C29  C38  SING  N  N  34  
9BJ  N30  C31  SING  N  N  35  
9BJ  N30  C35  SING  N  N  36  
9BJ  C31  N32  SING  N  N  37  
9BJ  C31  O37  DOUB  N  N  38  
9BJ  N32  C33  SING  N  N  39  
9BJ  C33  C34  SING  N  N  40  
9BJ  C33  O36  DOUB  N  N  41  
9BJ  C34  C35  DOUB  N  N  42  
9BJ  C38  O39  SING  N  N  43  
9BJ  C10  H1   SING  N  N  44  
9BJ  C13  H2   SING  N  N  45  
9BJ  C21  H3   SING  N  N  46  
9BJ  C22  H4   SING  N  N  47  
9BJ  C22  H5   SING  N  N  48  
9BJ  C04  H6   SING  N  N  49  
9BJ  C04  H7   SING  N  N  50  
9BJ  C05  H8   SING  N  N  51  
9BJ  C06  H9   SING  N  N  52  
9BJ  C08  H10  SING  N  N  53  
9BJ  O09  H11  SING  N  N  54  
9BJ  C12  H12  SING  N  N  55  
9BJ  N15  H13  SING  N  N  56  
9BJ  C23  H14  SING  N  N  57  
9BJ  C23  H15  SING  N  N  58  
9BJ  O27  H16  SING  N  N  59  
9BJ  O28  H17  SING  N  N  60  
9BJ  C29  H18  SING  N  N  61  
9BJ  N32  H19  SING  N  N  62  
9BJ  C34  H20  SING  N  N  63  
9BJ  C35  H21  SING  N  N  64  
9BJ  C38  H22  SING  N  N  65  
9BJ  O39  H23  SING  N  N  66  
9BJ  O40  H24  SING  N  N  67  
#   #
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
9BJ  SMILES            ACDLabs               12.01  "C3(C(C1C(COP(=O)(OC(CCOP(O1)(=O)O)C(C(O)N2C(NC(C=C2)=O)=O)O)O)O3)O)N4C=CC(NC4=O)=O"  
9BJ  InChI             InChI                 1.03   "InChI=1S/C18H24N4O16P2/c23-10-1-4-21(17(28)19-10)15(27)12(25)8-3-6-34-39(30,31)38-14-9(7-35-40(32,33)37-8)36-16(13(14)26)22-5-2-11(24)20-18(22)29/h1-2,4-5,8-9,12-16,25-27H,3,6-7H2,(H,30,31)(H,32,33)(H,19,23,28)(H,20,24,29)/t8-,9-,12-,13-,14-,15-,16-/m1/s1"  
9BJ  InChIKey          InChI                 1.03   SDBXSRQCWCPJQL-WXFFCYTBSA-N  
9BJ  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]([C@@H](O)N1C=CC(=O)NC1=O)[C@H]2CCO[P](O)(=O)O[C@H]3[C@@H](O)[C@@H](O[C@@H]3CO[P](O)(=O)O2)N4C=CC(=O)NC4=O"  
9BJ  SMILES            CACTVS                3.385  "O[CH]([CH](O)N1C=CC(=O)NC1=O)[CH]2CCO[P](O)(=O)O[CH]3[CH](O)[CH](O[CH]3CO[P](O)(=O)O2)N4C=CC(=O)NC4=O"  
9BJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1COP(=O)(O[C@@H]2[C@@H](COP(=O)(O[C@H]1[C@H]([C@H](N3C=CC(=O)NC3=O)O)O)O)O[C@H]([C@@H]2O)N4C=CC(=O)NC4=O)O"  
9BJ  SMILES            "OpenEye OEToolkits"  2.0.6  "C1COP(=O)(OC2C(COP(=O)(OC1C(C(N3C=CC(=O)NC3=O)O)O)O)OC(C2O)N4C=CC(=O)NC4=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
9BJ  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione"  
9BJ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "1-[(1~{S},7~{R},12~{R},14~{R},15~{R})-7-[(1~{R},2~{R})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-1,2-bis(oxidanyl)ethyl]-3,9,15-tris(oxidanyl)-3,9-bis(oxidanylidene)-2,4,8,10,13-pentaoxa-3$l^{5},9$l^{5}-diphosphabicyclo[10.3.0]pentadecan-14-yl]pyrimidine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
9BJ  "Create component"  2017-04-17  RCSB  
9BJ  "Initial release"   2017-09-27  RCSB  
9BJ  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     9BJ
_pdbx_chem_comp_synonyms.name        "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
