data_RPD
#

_chem_comp.id                                   RPD
_chem_comp.name                                 "(C8-R)-HYDANTOCIDIN 5'-PHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H22 N3 O13 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL]
PHOSPHATE
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_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                       459.300
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    RPD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1QF4
_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
RPD  O1P     O1P   O  0  1  N  N  N  25.212  11.748  23.784  -1.348  -1.066  -6.653  O1P     RPD   1  
RPD  O2P     O2P   O  0  1  N  N  N  27.238  12.877  23.098  -2.179   1.269  -7.129  O2P     RPD   2  
RPD  O3P     O3P   O  0  1  N  N  N  25.068  13.594  22.275   0.320   0.588  -7.575  O3P     RPD   3  
RPD  P       P     P  0  1  N  N  N  25.780  13.051  23.420  -0.953   0.359  -6.617  P       RPD   4  
RPD  "O5'"   O5*   O  0  1  N  N  N  25.668  14.053  24.698  -0.571   0.773  -5.109  "O5'"   RPD   5  
RPD  "C5'"   C5*   C  0  1  N  N  N  26.240  13.795  25.957   0.517  -0.064  -4.714  "C5'"   RPD   6  
RPD  "C4'"   C4*   C  0  1  N  N  R  27.053  14.986  26.437   0.931   0.278  -3.281  "C4'"   RPD   7  
RPD  "O4'"   O4*   O  0  1  N  N  N  28.289  15.046  25.744  -0.160   0.041  -2.375  "O4'"   RPD   8  
RPD  "C3'"   C3*   C  0  1  N  N  S  26.386  16.320  26.203   2.065  -0.664  -2.806  "C3'"   RPD   9  
RPD  "O3'"   O3*   O  0  1  N  N  N  26.806  17.253  27.211   3.347  -0.155  -3.177  "O3'"   RPD  10  
RPD  "C2'"   C2*   C  0  1  N  N  R  26.958  16.747  24.805   1.866  -0.615  -1.265  "C2'"   RPD  11  
RPD  "O2'"   O2*   O  0  1  N  N  N  27.106  18.181  24.778   2.535   0.514  -0.701  "O2'"   RPD  12  
RPD  "C1'"   C1*   C  0  1  N  N  S  28.351  16.074  24.691   0.341  -0.468  -1.143  "C1'"   RPD  13  
RPD  N1      N1    N  0  1  N  N  N  28.402  15.432  23.483  -0.276  -1.752  -0.801  N1      RPD  14  
RPD  C2      C2    C  0  1  N  N  N  29.507  15.838  22.756  -0.889  -1.573   0.385  C2      RPD  15  
RPD  O2      O2    O  0  1  N  N  N  29.787  15.439  21.686  -1.506  -2.445   0.965  O2      RPD  16  
RPD  N3      N3    N  0  1  N  N  N  30.213  16.769  23.473  -0.742  -0.327   0.852  N3      RPD  17  
RPD  C4      C4    C  0  1  N  N  N  29.513  16.936  24.675  -0.018   0.437   0.008  C4      RPD  18  
RPD  O4      O4    O  0  1  N  N  N  29.909  17.731  25.542   0.284   1.602   0.149  O4      RPD  19  
RPD  C5A     C5A   C  0  1  N  N  N  31.454  17.447  23.039  -1.303   0.147   2.120  C5A     RPD  20  
RPD  C6A     C6A   C  0  1  N  N  N  31.148  18.892  22.595  -0.291  -0.084   3.244  C6A     RPD  21  
RPD  C7A     C7A   C  0  1  N  N  N  30.001  18.931  21.555  -0.876   0.411   4.567  C7A     RPD  22  
RPD  C8A     C8A   C  0  1  N  N  R  29.778  20.402  21.112   0.168   0.263   5.675  C8A     RPD  23  
RPD  C9A     C9A   C  0  1  N  N  N  28.331  20.655  20.700   0.458  -1.197   5.899  C9A     RPD  24  
RPD  OJA     O91A  O  0  1  N  N  N  27.308  20.036  21.332  -0.160  -1.860   6.888  OJA     RPD  25  
RPD  OKA     O92A  O  0  1  N  N  N  28.087  21.519  19.685   1.248  -1.773   5.188  OKA     RPD  26  
RPD  NAA     N10A  N  0  1  N  N  N  30.623  20.798  19.931  -0.346   0.857   6.916  NAA     RPD  27  
RPD  OAA     O10A  O  0  1  N  N  N  31.419  21.964  20.297  -1.705   0.345   7.095  OAA     RPD  28  
RPD  CBA     C11A  C  0  1  N  N  N  31.514  19.716  19.497  -0.466   2.301   6.675  CBA     RPD  29  
RPD  OBA     O11A  O  0  1  N  N  N  32.302  20.114  18.379   0.816   2.838   6.349  OBA     RPD  30  
RPD  HO2P    HO2P  H  0  0  N  N  N  27.605  13.720  22.862  -2.375   0.990  -8.034  HO2P    RPD  31  
RPD  HO3P    HO3P  H  0  0  N  N  N  25.435  14.437  22.039   0.545   1.527  -7.523  HO3P    RPD  32  
RPD  "H5'1"  1H5*  H  0  0  N  N  N  25.470  13.493  26.705   1.361   0.096  -5.384  "H5'1"  RPD  33  
RPD  "H5'2"  2H5*  H  0  0  N  N  N  26.845  12.858  25.950   0.207  -1.108  -4.762  "H5'2"  RPD  34  
RPD  H4      H4    H  0  1  N  N  N  27.173  14.823  27.533   1.253   1.318  -3.220  H4      RPD  35  
RPD  H3      H3    H  0  1  N  N  N  25.272  16.281  26.237   1.921  -1.675  -3.188  H3      RPD  36  
RPD  "HO3'"  HO3*  H  0  0  N  N  N  26.386  18.092  27.063   3.362  -0.112  -4.143  "HO3'"  RPD  37  
RPD  H2      H2    H  0  1  N  N  N  26.289  16.443  23.965   2.207  -1.540  -0.799  H2      RPD  38  
RPD  "HO2'"  HO2*  H  0  0  N  N  N  27.452  18.439  23.931   3.477   0.405  -0.892  "HO2'"  RPD  39  
RPD  HN1     HN1   H  0  1  N  N  N  27.537  15.552  22.954  -0.249  -2.569  -1.325  HN1     RPD  40  
RPD  H51     1H5   H  0  1  N  N  N  32.243  17.412  23.825  -2.221  -0.397   2.338  H51     RPD  41  
RPD  H52     2H5   H  0  1  N  N  N  31.986  16.872  22.245  -1.522   1.212   2.043  H52     RPD  42  
RPD  H61     1H6   H  0  1  N  N  N  30.931  19.550  23.468   0.626   0.460   3.025  H61     RPD  43  
RPD  H62     2H6   H  0  1  N  N  N  32.062  19.405  22.215  -0.071  -1.149   3.320  H62     RPD  44  
RPD  H71     1H7   H  0  1  N  N  N  30.185  18.249  20.692  -1.758  -0.177   4.818  H71     RPD  45  
RPD  H72     2H7   H  0  1  N  N  N  29.066  18.453  21.932  -1.156   1.460   4.470  H72     RPD  46  
RPD  H81     1H8   H  0  1  N  N  N  30.060  21.004  22.006   1.084   0.775   5.380  H81     RPD  47  
RPD  H91     H91   H  0  1  N  N  N  26.407  20.193  21.075   0.026  -2.798   7.032  H91     RPD  48  
RPD  H10     H10   H  0  1  N  N  N  31.952  22.213  19.551  -1.628  -0.607   7.240  H10     RPD  49  
RPD  H111    1H11  H  0  0  N  N  N  32.149  19.347  20.335  -0.846   2.788   7.573  H111    RPD  50  
RPD  H112    2H11  H  0  0  N  N  N  30.948  18.778  19.286  -1.154   2.475   5.848  H112    RPD  51  
RPD  H11     H11   H  0  1  N  N  N  32.878  19.413  18.098   0.693   3.785   6.199  H11     RPD  52  
#   #
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
RPD  O1P    P       DOUB  N  N   1  
RPD  O2P    P       SING  N  N   2  
RPD  O2P    HO2P    SING  N  N   3  
RPD  O3P    P       SING  N  N   4  
RPD  O3P    HO3P    SING  N  N   5  
RPD  P      "O5'"   SING  N  N   6  
RPD  "O5'"  "C5'"   SING  N  N   7  
RPD  "C5'"  "C4'"   SING  N  N   8  
RPD  "C5'"  "H5'1"  SING  N  N   9  
RPD  "C5'"  "H5'2"  SING  N  N  10  
RPD  "C4'"  "O4'"   SING  N  N  11  
RPD  "C4'"  "C3'"   SING  N  N  12  
RPD  "C4'"  H4      SING  N  N  13  
RPD  "O4'"  "C1'"   SING  N  N  14  
RPD  "C3'"  "O3'"   SING  N  N  15  
RPD  "C3'"  "C2'"   SING  N  N  16  
RPD  "C3'"  H3      SING  N  N  17  
RPD  "O3'"  "HO3'"  SING  N  N  18  
RPD  "C2'"  "O2'"   SING  N  N  19  
RPD  "C2'"  "C1'"   SING  N  N  20  
RPD  "C2'"  H2      SING  N  N  21  
RPD  "O2'"  "HO2'"  SING  N  N  22  
RPD  "C1'"  N1      SING  N  N  23  
RPD  "C1'"  C4      SING  N  N  24  
RPD  N1     C2      SING  N  N  25  
RPD  N1     HN1     SING  N  N  26  
RPD  C2     O2      DOUB  N  N  27  
RPD  C2     N3      SING  N  N  28  
RPD  N3     C4      SING  N  N  29  
RPD  N3     C5A     SING  N  N  30  
RPD  C4     O4      DOUB  N  N  31  
RPD  C5A    C6A     SING  N  N  32  
RPD  C5A    H51     SING  N  N  33  
RPD  C5A    H52     SING  N  N  34  
RPD  C6A    C7A     SING  N  N  35  
RPD  C6A    H61     SING  N  N  36  
RPD  C6A    H62     SING  N  N  37  
RPD  C7A    C8A     SING  N  N  38  
RPD  C7A    H71     SING  N  N  39  
RPD  C7A    H72     SING  N  N  40  
RPD  C8A    C9A     SING  N  N  41  
RPD  C8A    NAA     SING  N  N  42  
RPD  C8A    H81     SING  N  N  43  
RPD  C9A    OJA     SING  N  N  44  
RPD  C9A    OKA     DOUB  N  N  45  
RPD  OJA    H91     SING  N  N  46  
RPD  NAA    OAA     SING  N  N  47  
RPD  NAA    CBA     SING  N  N  48  
RPD  OAA    H10     SING  N  N  49  
RPD  CBA    OBA     SING  N  N  50  
RPD  CBA    H111    SING  N  N  51  
RPD  CBA    H112    SING  N  N  52  
RPD  OBA    H11     SING  N  N  53  
#   #
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
RPD  SMILES            ACDLabs               10.04  "O=C(O)C(N(O)CO)CCCN2C(=O)C1(OC(C(O)C1O)COP(=O)(O)O)NC2=O"  
RPD  SMILES_CANONICAL  CACTVS                3.341  "OCN(O)[C@H](CCCN1C(=O)N[C@@]2(O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O"  
RPD  SMILES            CACTVS                3.341  "OCN(O)[CH](CCCN1C(=O)N[C]2(O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O"  
RPD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C(C[C@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)NC1=O"  
RPD  SMILES            "OpenEye OEToolkits"  1.5.0  "C(CC(C(=O)O)N(CO)O)CN1C(=O)C2(C(C(C(O2)COP(=O)(O)O)O)O)NC1=O"  
RPD  InChI             InChI                 1.03   "InChI=1S/C13H22N3O13P/c17-5-16(24)6(10(20)21)2-1-3-15-11(22)13(14-12(15)23)9(19)8(18)7(29-13)4-28-30(25,26)27/h6-9,17-19,24H,1-5H2,(H,14,23)(H,20,21)(H2,25,26,27)/t6-,7-,8-,9-,13+/m1/s1"  
RPD  InChIKey          InChI                 1.03   MAXSFYCTFIBEAR-OJMIUMIFSA-N  
#   #
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
RPD  "SYSTEMATIC NAME"  ACDLabs               10.04  "5-{(5S,7R,8S,9R)-8,9-dihydroxy-2,4-dioxo-7-[(phosphonooxy)methyl]-6-oxa-1,3-diazaspiro[4.4]non-3-yl}-N-hydroxy-N-(hydroxymethyl)-D-norvaline"  
RPD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R)-5-[(2R,3S,4R,5S)-3,4-dihydroxy-7,9-dioxo-2-(phosphonooxymethyl)-1-oxa-6,8-diazaspiro[4.4]nonan-8-yl]-2-(hydroxy-(hydroxymethyl)amino)pentanoic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RPD  "Create component"   1999-07-08  RCSB  
RPD  "Modify descriptor"  2011-06-04  RCSB  
RPD  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     RPD
_pdbx_chem_comp_synonyms.name        "[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
