data_3DU
#

_chem_comp.id                                   3DU
_chem_comp.name                                 "4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H14 N O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "3-deazauridine 5'-monophosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-12-05
_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                       323.193
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3DU
_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       4NT0
_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
3DU  OP3    OP3    O  0  1  N  N  N  7.433   4.151  -10.300  -5.194  -0.023  -0.395  OP3    3DU   1  
3DU  P      P      P  0  1  N  N  N  6.324   3.359   -9.665  -4.189  -0.994   0.093  P      3DU   2  
3DU  OP1    OP1    O  0  1  N  N  N  6.939   2.163   -8.928  -4.770  -1.766   1.380  OP1    3DU   3  
3DU  OP2    OP2    O  0  1  N  N  N  5.429   4.314   -8.866  -3.863  -2.059  -1.070  OP2    3DU   4  
3DU  "O5'"  "O5'"  O  0  1  N  N  N  5.391   2.767  -10.814  -2.842  -0.212   0.499  "O5'"  3DU   5  
3DU  "C5'"  "C5'"  C  0  1  N  N  N  5.833   1.696  -11.641  -2.143   0.653  -0.399  "C5'"  3DU   6  
3DU  "C4'"  "C4'"  C  0  1  N  N  R  4.717   1.166  -12.506  -0.912   1.229   0.302  "C4'"  3DU   7  
3DU  "O4'"  "O4'"  O  0  1  N  N  N  5.235   0.074  -13.316   0.075   0.197   0.516  "O4'"  3DU   8  
3DU  "C3'"  "C3'"  C  0  1  N  N  S  3.520   0.595  -11.751  -0.210   2.264  -0.606  "C3'"  3DU   9  
3DU  "O3'"  "O3'"  O  0  1  N  N  N  2.350   0.737  -12.553  -0.592   3.591  -0.240  "O3'"  3DU  10  
3DU  "C2'"  "C2'"  C  0  1  N  N  R  3.874  -0.886  -11.646   1.295   2.040  -0.337  "C2'"  3DU  11  
3DU  "O2'"  "O2'"  O  0  1  N  N  N  2.757  -1.741  -11.457   1.888   3.222   0.203  "O2'"  3DU  12  
3DU  "C1'"  "C1'"  C  0  1  N  N  R  4.558  -1.129  -12.995   1.324   0.897   0.702  "C1'"  3DU  13  
3DU  N1     N1     N  0  1  N  N  N  5.558  -2.213  -13.004   2.454   0.001   0.442  N1     3DU  14  
3DU  C2     C2     C  0  1  N  N  N  5.428  -3.251  -13.856   2.517  -0.664  -0.726  C2     3DU  15  
3DU  O2     O2     O  0  1  N  N  N  4.376  -3.326  -14.682   1.636  -0.517  -1.559  O2     3DU  16  
3DU  C3     C3     C  0  1  N  N  N  6.382  -4.296  -13.896   3.591  -1.523  -0.989  C3     3DU  17  
3DU  C4     C4     C  0  1  N  N  N  7.482  -4.215  -13.035   4.579  -1.676  -0.034  C4     3DU  18  
3DU  O4     O4     O  0  1  N  N  N  8.438  -5.191  -13.041   5.631  -2.500  -0.260  O4     3DU  19  
3DU  C5     C5     C  0  1  N  N  N  7.616  -3.120  -12.161   4.476  -0.963   1.176  C5     3DU  20  
3DU  C6     C6     C  0  1  N  N  N  6.629  -2.122  -12.176   3.425  -0.141   1.383  C6     3DU  21  
3DU  H1     H1     H  0  1  N  N  N  7.883   2.179   -9.030  -5.583  -2.260   1.209  H1     3DU  22  
3DU  H2     H2     H  0  1  N  N  N  5.764   5.200   -8.941  -3.210  -2.727  -0.820  H2     3DU  23  
3DU  H3     H3     H  0  1  N  N  N  6.207   0.882  -11.002  -1.830   0.088  -1.278  H3     3DU  24  
3DU  H4     H4     H  0  1  N  N  N  6.646   2.057  -12.288  -2.801   1.466  -0.706  H4     3DU  25  
3DU  H5     H5     H  0  1  N  N  N  4.363   1.975  -13.163  -1.196   1.687   1.250  H5     3DU  26  
3DU  H6     H6     H  0  1  N  N  N  3.417   1.054  -10.757  -0.444   2.073  -1.653  H6     3DU  27  
3DU  H7     H7     H  0  1  N  N  N  1.601   0.383  -12.087  -0.181   4.281  -0.779  H7     3DU  28  
3DU  H8     H8     H  0  1  N  N  N  4.610  -1.025  -10.840   1.806   1.740  -1.252  H8     3DU  29  
3DU  H9     H9     H  0  1  N  N  N  2.360  -1.562  -10.613   1.843   3.989  -0.385  H9     3DU  30  
3DU  H10    H10    H  0  1  N  N  N  3.784  -1.341  -13.747   1.385   1.303   1.711  H10    3DU  31  
3DU  H11    H11    H  0  1  N  N  N  6.264  -5.131  -14.571   3.646  -2.059  -1.925  H11    3DU  32  
3DU  H12    H12    H  0  1  N  N  N  9.108  -4.982  -12.401   6.265  -2.537   0.470  H12    3DU  33  
3DU  H13    H13    H  0  1  N  N  N  8.461  -3.049  -11.492   5.237  -1.069   1.934  H13    3DU  34  
3DU  H14    H14    H  0  1  N  N  N  6.723  -1.270  -11.519   3.352   0.408   2.310  H14    3DU  35  
#   #
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
3DU  O2     C2     DOUB  N  N   1  
3DU  C3     C2     SING  N  N   2  
3DU  C3     C4     DOUB  N  N   3  
3DU  C2     N1     SING  N  N   4  
3DU  "O4'"  "C1'"  SING  N  N   5  
3DU  "O4'"  "C4'"  SING  N  N   6  
3DU  O4     C4     SING  N  N   7  
3DU  C4     C5     SING  N  N   8  
3DU  N1     "C1'"  SING  N  N   9  
3DU  N1     C6     SING  N  N  10  
3DU  "C1'"  "C2'"  SING  N  N  11  
3DU  "O3'"  "C3'"  SING  N  N  12  
3DU  "C4'"  "C3'"  SING  N  N  13  
3DU  "C4'"  "C5'"  SING  N  N  14  
3DU  C6     C5     DOUB  N  N  15  
3DU  "C3'"  "C2'"  SING  N  N  16  
3DU  "C2'"  "O2'"  SING  N  N  17  
3DU  "C5'"  "O5'"  SING  N  N  18  
3DU  "O5'"  P      SING  N  N  19  
3DU  OP3    P      DOUB  N  N  20  
3DU  P      OP1    SING  N  N  21  
3DU  P      OP2    SING  N  N  22  
3DU  OP1    H1     SING  N  N  23  
3DU  OP2    H2     SING  N  N  24  
3DU  "C5'"  H3     SING  N  N  25  
3DU  "C5'"  H4     SING  N  N  26  
3DU  "C4'"  H5     SING  N  N  27  
3DU  "C3'"  H6     SING  N  N  28  
3DU  "O3'"  H7     SING  N  N  29  
3DU  "C2'"  H8     SING  N  N  30  
3DU  "O2'"  H9     SING  N  N  31  
3DU  "C1'"  H10    SING  N  N  32  
3DU  C3     H11    SING  N  N  33  
3DU  O4     H12    SING  N  N  34  
3DU  C5     H13    SING  N  N  35  
3DU  C6     H14    SING  N  N  36  
#   #
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
3DU  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OC(N1C(=O)C=C(O)C=C1)C(O)C2O"  
3DU  InChI             InChI                 1.03   "InChI=1S/C10H14NO9P/c12-5-1-2-11(7(13)3-5)10-9(15)8(14)6(20-10)4-19-21(16,17)18/h1-3,6,8-10,12,14-15H,4H2,(H2,16,17,18)/t6-,8-,9-,10-/m1/s1"  
3DU  InChIKey          InChI                 1.03   BMAAJONJGSMHCR-PEBGCTIMSA-N  
3DU  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O"  
3DU  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O"  
3DU  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)C=C1O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
3DU  SMILES            "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)C=C1O)C2C(C(C(O2)COP(=O)(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
3DU  "SYSTEMATIC NAME"  ACDLabs               12.01  "4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one"  
3DU  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4-oxidanyl-2-oxidanylidene-pyridin-1-yl)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
3DU  "Create component"  2013-12-05  RCSB  
3DU  "Initial release"   2013-12-18  RCSB  
3DU  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3DU
_pdbx_chem_comp_synonyms.name        "3-deazauridine 5'-monophosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
