data_Z7P
#

_chem_comp.id                                   Z7P
_chem_comp.name                                 "(2R,3R,4S,5S,6R)-3,4-dihydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyloxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H33 N4 O20 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-04-12
_chem_comp.pdbx_modified_date                   2021-04-23
_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                       778.444
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Z7P
_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       7MFP
_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
Z7P  O41  O1   O  0  1  N  N  N  -17.487   5.191  32.431  -7.295   5.741  -2.541  O41  Z7P   1  
Z7P  C41  C1   C  0  1  N  N  N  -16.807   5.509  31.445  -7.201   4.868  -1.698  C41  Z7P   2  
Z7P  C51  C2   C  0  1  N  N  N  -16.177   4.551  30.640  -7.022   5.207  -0.335  C51  Z7P   3  
Z7P  C61  C3   C  0  1  N  N  N  -15.400   4.970  29.590  -6.922   4.219   0.580  C61  Z7P   4  
Z7P  N31  N1   N  0  1  N  N  N  -16.612   6.814  31.148  -7.273   3.569  -2.053  N31  Z7P   5  
Z7P  C21  C4   C  0  1  N  N  N  -15.852   7.251  30.137  -7.170   2.604  -1.120  C21  Z7P   6  
Z7P  O21  O2   O  0  1  N  N  N  -15.692   8.483  29.940  -7.237   1.437  -1.454  O21  Z7P   7  
Z7P  N11  N2   N  0  1  N  N  N  -15.237   6.302  29.309  -6.994   2.913   0.178  N11  Z7P   8  
Z7P  C1   C5   C  0  1  N  N  R  -14.374   6.718  28.203  -6.885   1.841   1.170  C1   Z7P   9  
Z7P  O4   O3   O  0  1  N  N  N  -14.676   6.058  26.978  -5.926   0.849   0.744  O4   Z7P  10  
Z7P  C2   C6   C  0  1  N  N  R  -12.954   6.243  28.468  -8.212   1.045   1.262  C2   Z7P  11  
Z7P  O2   O4   O  0  1  N  N  N  -12.319   7.205  29.250  -9.117   1.666   2.178  O2   Z7P  12  
Z7P  C3   C7   C  0  1  N  N  S  -12.336   6.131  27.113  -7.732  -0.324   1.803  C3   Z7P  13  
Z7P  O3   O5   O  0  1  N  N  N  -11.950   7.474  26.692  -7.923  -0.398   3.217  O3   Z7P  14  
Z7P  C4   C8   C  0  1  N  N  R  -13.515   5.700  26.221  -6.231  -0.362   1.456  C4   Z7P  15  
Z7P  C5   C9   C  0  1  N  N  N  -13.559   4.225  25.843  -5.933  -1.574   0.571  C5   Z7P  16  
Z7P  O5   O6   O  0  1  N  N  N  -13.459   3.472  27.059  -4.526  -1.658   0.336  O5   Z7P  17  
Z7P  P    P1   P  0  1  N  N  N  -12.668   2.169  27.231  -3.853  -2.816  -0.558  P    Z7P  18  
Z7P  O1P  O7   O  0  1  N  N  N  -11.224   2.111  26.802  -4.253  -4.140  -0.031  O1P  Z7P  19  
Z7P  O2P  O8   O  0  1  N  N  N  -12.760   1.808  28.690  -4.348  -2.672  -2.083  O2P  Z7P  20  
Z7P  OPP  O9   O  0  1  N  N  N  -13.410   0.956  26.507  -2.250  -2.677  -0.498  OPP  Z7P  21  
Z7P  P2   P2   P  0  1  N  N  N  -13.331   0.361  25.032  -1.028  -3.648  -0.891  P2   Z7P  22  
Z7P  O3P  O10  O  0  1  N  N  N  -12.993   1.449  24.019  -1.350  -5.035  -0.487  O3P  Z7P  23  
Z7P  O4P  O11  O  0  1  N  N  N  -12.594  -0.922  25.113  -0.790  -3.594  -2.483  O4P  Z7P  24  
Z7P  O1G  O12  O  0  1  N  N  N  -14.893  -0.106  24.801   0.307  -3.165  -0.132  O1G  Z7P  25  
Z7P  C1G  C10  C  0  1  N  N  R  -15.915   0.879  24.913   1.541  -3.884  -0.193  C1G  Z7P  26  
Z7P  O5G  O13  O  0  1  N  N  N  -16.261   1.296  23.583   2.313  -3.413  -1.298  O5G  Z7P  27  
Z7P  C5G  C11  C  0  1  N  N  R  -16.912   0.330  22.773   2.617  -2.017  -1.246  C5G  Z7P  28  
Z7P  C6G  C12  C  0  1  N  N  N  -17.094   0.928  21.379   3.418  -1.622  -2.488  C6G  Z7P  29  
Z7P  C4G  C13  C  0  1  N  N  S  -18.285   0.021  23.419   3.443  -1.724   0.009  C4G  Z7P  30  
Z7P  C3G  C14  C  0  1  N  N  S  -18.090  -0.539  24.859   2.659  -2.177   1.245  C3G  Z7P  31  
Z7P  O3G  O14  O  0  1  N  N  N  -19.324  -0.467  25.573   3.453  -1.974   2.416  O3G  Z7P  32  
Z7P  C2G  C15  C  0  1  N  N  R  -17.103   0.304  25.705   2.323  -3.665   1.105  C2G  Z7P  33  
Z7P  O2G  O15  O  0  1  N  N  N  -16.572  -0.395  26.831   1.529  -4.082   2.217  O2G  Z7P  34  
Z7P  N4A  N3   N  0  1  N  N  N  -18.963  -0.939  22.500   3.706  -0.285   0.097  N4A  Z7P  35  
Z7P  C4A  C16  C  0  1  N  N  N  -19.673  -1.907  22.914   4.923   0.151   0.101  C4A  Z7P  36  
Z7P  C4L  C17  C  0  1  Y  N  N  -20.280  -2.811  21.931   5.188   1.600   0.190  C4L  Z7P  37  
Z7P  C3L  C18  C  0  1  Y  N  N  -20.139  -2.500  20.485   4.133   2.523   0.276  C3L  Z7P  38  
Z7P  O3L  O16  O  0  1  N  N  N  -19.428  -1.379  20.104   2.843   2.100   0.275  O3L  Z7P  39  
Z7P  C2L  C19  C  0  1  Y  N  N  -20.772  -3.404  19.512   4.432   3.876   0.363  C2L  Z7P  40  
Z7P  C2A  C20  C  0  1  N  N  N  -20.672  -3.178  18.047   3.313   4.881   0.457  C2A  Z7P  41  
Z7P  C5L  C21  C  0  1  Y  N  N  -21.024  -4.019  22.340   6.498   2.094   0.196  C5L  Z7P  42  
Z7P  C6L  C22  C  0  1  Y  N  N  -21.561  -4.807  21.317   6.700   3.456   0.280  C6L  Z7P  43  
Z7P  N1L  N4   N  0  1  Y  N  N  -21.436  -4.495  19.976   5.682   4.291   0.365  N1L  Z7P  44  
Z7P  C5B  C23  C  0  1  N  N  N  -21.210  -4.425  23.779   7.670   1.151   0.112  C5B  Z7P  45  
Z7P  OP4  O17  O  0  1  N  N  N  -22.025  -3.531  24.506   8.887   1.901   0.136  OP4  Z7P  46  
Z7P  PL   P3   P  0  1  N  N  N  -21.712  -3.372  26.082  10.341   1.215   0.063  PL   Z7P  47  
Z7P  OP1  O18  O  0  1  N  N  N  -22.703  -2.409  26.565  11.476   2.342   0.246  OP1  Z7P  48  
Z7P  OP2  O19  O  0  1  N  N  N  -20.325  -2.707  26.246  10.467   0.209   1.141  OP2  Z7P  49  
Z7P  OP3  O20  O  0  1  N  N  N  -21.687  -4.825  26.586  10.524   0.496  -1.365  OP3  Z7P  50  
Z7P  H1   H1   H  0  1  N  N  N  -16.301   3.498  30.843  -6.966   6.241  -0.032  H1   Z7P  51  
Z7P  H2   H2   H  0  1  N  N  N  -14.906   4.235  28.972  -6.784   4.458   1.624  H2   Z7P  52  
Z7P  H3   H3   H  0  1  N  N  N  -17.065   7.497  31.721  -7.400   3.329  -2.984  H3   Z7P  53  
Z7P  H4   H4   H  0  1  N  N  N  -14.389   7.812  28.085  -6.613   2.247   2.144  H4   Z7P  54  
Z7P  H5   H5   H  0  1  N  N  N  -12.973   5.260  28.962  -8.670   0.937   0.279  H5   Z7P  55  
Z7P  H6   H6   H  0  1  N  N  N  -12.738   7.248  30.102  -9.962   1.205   2.270  H6   Z7P  56  
Z7P  H7   H7   H  0  1  N  N  N  -11.507   5.408  27.081  -8.260  -1.137   1.304  H7   Z7P  57  
Z7P  H8   H8   H  0  1  N  N  N  -11.222   7.775  27.222  -8.846  -0.321   3.494  H8   Z7P  58  
Z7P  H9   H9   H  0  1  N  N  N  -13.480   6.294  25.296  -5.641  -0.414   2.370  H9   Z7P  59  
Z7P  H10  H10  H  0  1  N  N  N  -14.507   3.995  25.334  -6.273  -2.481   1.071  H10  Z7P  60  
Z7P  H11  H11  H  0  1  N  N  N  -12.717   3.981  25.178  -6.454  -1.467  -0.381  H11  Z7P  61  
Z7P  H12  H12  H  0  1  N  N  N  -11.891   1.622  29.026  -4.120  -1.827  -2.493  H12  Z7P  62  
Z7P  H13  H13  H  0  1  N  N  N  -11.911  -0.938  24.453  -0.574  -2.713  -2.818  H13  Z7P  63  
Z7P  H14  H14  H  0  1  N  N  N  -15.526   1.743  25.471   1.336  -4.947  -0.319  H14  Z7P  64  
Z7P  H15  H15  H  0  1  N  N  N  -16.323  -0.596  22.705   1.691  -1.444  -1.213  H15  Z7P  65  
Z7P  H16  H16  H  0  1  N  N  N  -16.108   1.140  20.939   4.345  -2.196  -2.520  H16  Z7P  66  
Z7P  H17  H17  H  0  1  N  N  N  -17.634   0.213  20.741   2.830  -1.831  -3.381  H17  Z7P  67  
Z7P  H18  H18  H  0  1  N  N  N  -17.671   1.862  21.453   3.651  -0.558  -2.447  H18  Z7P  68  
Z7P  H19  H19  H  0  1  N  N  N  -18.869   0.952  23.477   4.388  -2.265  -0.041  H19  Z7P  69  
Z7P  H20  H20  H  0  1  N  N  N  -17.727  -1.576  24.799   1.738  -1.600   1.324  H20  Z7P  70  
Z7P  H21  H21  H  0  1  N  N  N  -19.621  -1.345  25.782   3.017  -2.240   3.237  H21  Z7P  71  
Z7P  H22  H22  H  0  1  N  N  N  -17.674   1.165  26.082   3.245  -4.246   1.076  H22  Z7P  72  
Z7P  H23  H23  H  0  1  N  N  N  -15.977   0.174  27.306   1.275  -5.015   2.192  H23  Z7P  73  
Z7P  H24  H24  H  0  1  N  N  N  -19.827  -2.062  23.972   5.746  -0.545   0.040  H24  Z7P  74  
Z7P  H25  H25  H  0  1  N  N  N  -19.102  -0.933  20.877   2.489   1.917   1.156  H25  Z7P  75  
Z7P  H26  H26  H  0  1  N  N  N  -21.190  -3.989  17.514   3.022   5.195  -0.545  H26  Z7P  76  
Z7P  H27  H27  H  0  1  N  N  N  -21.139  -2.215  17.792   2.459   4.428   0.959  H27  Z7P  77  
Z7P  H28  H28  H  0  1  N  N  N  -19.613  -3.162  17.750   3.651   5.748   1.025  H28  Z7P  78  
Z7P  H29  H29  H  0  1  N  N  N  -22.100  -5.703  21.588   7.707   3.844   0.286  H29  Z7P  79  
Z7P  H30  H30  H  0  1  N  N  N  -21.675  -5.422  23.804   7.648   0.467   0.960  H30  Z7P  80  
Z7P  H31  H31  H  0  1  N  N  N  -20.222  -4.469  24.261   7.613   0.582  -0.816  H31  Z7P  81  
Z7P  H32  H32  H  0  1  N  N  N  -22.262  -1.620  26.858  12.380   1.999   0.213  H32  Z7P  82  
Z7P  H33  H33  H  0  1  N  N  N  -20.817  -5.036  26.904  10.454   1.097  -2.120  H33  Z7P  83  
#   #
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
Z7P  C2A  C2L  SING  N  N   1  
Z7P  C2L  N1L  DOUB  Y  N   2  
Z7P  C2L  C3L  SING  Y  N   3  
Z7P  N1L  C6L  SING  Y  N   4  
Z7P  O3L  C3L  SING  N  N   5  
Z7P  C3L  C4L  DOUB  Y  N   6  
Z7P  C6L  C5L  DOUB  Y  N   7  
Z7P  C6G  C5G  SING  N  N   8  
Z7P  C4L  C5L  SING  Y  N   9  
Z7P  C4L  C4A  SING  N  N  10  
Z7P  C5L  C5B  SING  N  N  11  
Z7P  N4A  C4A  DOUB  N  N  12  
Z7P  N4A  C4G  SING  N  N  13  
Z7P  C5G  C4G  SING  N  N  14  
Z7P  C5G  O5G  SING  N  N  15  
Z7P  C4G  C3G  SING  N  N  16  
Z7P  O5G  C1G  SING  N  N  17  
Z7P  C5B  OP4  SING  N  N  18  
Z7P  O3P  P2   DOUB  N  N  19  
Z7P  OP4  PL   SING  N  N  20  
Z7P  O1G  C1G  SING  N  N  21  
Z7P  O1G  P2   SING  N  N  22  
Z7P  C3G  O3G  SING  N  N  23  
Z7P  C3G  C2G  SING  N  N  24  
Z7P  C1G  C2G  SING  N  N  25  
Z7P  P2   O4P  SING  N  N  26  
Z7P  P2   OPP  SING  N  N  27  
Z7P  C2G  O2G  SING  N  N  28  
Z7P  C5   C4   SING  N  N  29  
Z7P  C5   O5   SING  N  N  30  
Z7P  PL   OP2  DOUB  N  N  31  
Z7P  PL   OP1  SING  N  N  32  
Z7P  PL   OP3  SING  N  N  33  
Z7P  C4   O4   SING  N  N  34  
Z7P  C4   C3   SING  N  N  35  
Z7P  OPP  P    SING  N  N  36  
Z7P  O3   C3   SING  N  N  37  
Z7P  O1P  P    DOUB  N  N  38  
Z7P  O4   C1   SING  N  N  39  
Z7P  O5   P    SING  N  N  40  
Z7P  C3   C2   SING  N  N  41  
Z7P  P    O2P  SING  N  N  42  
Z7P  C1   C2   SING  N  N  43  
Z7P  C1   N11  SING  N  N  44  
Z7P  C2   O2   SING  N  N  45  
Z7P  N11  C61  SING  N  N  46  
Z7P  N11  C21  SING  N  N  47  
Z7P  C61  C51  DOUB  N  N  48  
Z7P  O21  C21  DOUB  N  N  49  
Z7P  C21  N31  SING  N  N  50  
Z7P  C51  C41  SING  N  N  51  
Z7P  N31  C41  SING  N  N  52  
Z7P  C41  O41  DOUB  N  N  53  
Z7P  C51  H1   SING  N  N  54  
Z7P  C61  H2   SING  N  N  55  
Z7P  N31  H3   SING  N  N  56  
Z7P  C1   H4   SING  N  N  57  
Z7P  C2   H5   SING  N  N  58  
Z7P  O2   H6   SING  N  N  59  
Z7P  C3   H7   SING  N  N  60  
Z7P  O3   H8   SING  N  N  61  
Z7P  C4   H9   SING  N  N  62  
Z7P  C5   H10  SING  N  N  63  
Z7P  C5   H11  SING  N  N  64  
Z7P  O2P  H12  SING  N  N  65  
Z7P  O4P  H13  SING  N  N  66  
Z7P  C1G  H14  SING  N  N  67  
Z7P  C5G  H15  SING  N  N  68  
Z7P  C6G  H16  SING  N  N  69  
Z7P  C6G  H17  SING  N  N  70  
Z7P  C6G  H18  SING  N  N  71  
Z7P  C4G  H19  SING  N  N  72  
Z7P  C3G  H20  SING  N  N  73  
Z7P  O3G  H21  SING  N  N  74  
Z7P  C2G  H22  SING  N  N  75  
Z7P  O2G  H23  SING  N  N  76  
Z7P  C4A  H24  SING  N  N  77  
Z7P  O3L  H25  SING  N  N  78  
Z7P  C2A  H26  SING  N  N  79  
Z7P  C2A  H27  SING  N  N  80  
Z7P  C2A  H28  SING  N  N  81  
Z7P  C6L  H29  SING  N  N  82  
Z7P  C5B  H30  SING  N  N  83  
Z7P  C5B  H31  SING  N  N  84  
Z7P  OP1  H32  SING  N  N  85  
Z7P  OP3  H33  SING  N  N  86  
#   #
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
Z7P  SMILES            ACDLabs               12.01  "O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OC(C)C(/N=C/c3c(COP(=O)(O)O)cnc(C)c3O)C(O)C2O)C(O)C1O"  
Z7P  InChI             InChI                 1.03   "InChI=1S/C23H33N4O20P3/c1-9-16(29)12(11(5-24-9)7-42-48(35,36)37)6-25-15-10(2)44-22(20(33)18(15)31)46-50(40,41)47-49(38,39)43-8-13-17(30)19(32)21(45-13)27-4-3-14(28)26-23(27)34/h3-6,10,13,15,17-22,29-33H,7-8H2,1-2H3,(H,38,39)(H,40,41)(H,26,28,34)(H2,35,36,37)/b25-6+/t10-,13-,15-,17-,18+,19-,20-,21-,22-/m1/s1"  
Z7P  InChIKey          InChI                 1.03   YCGRRMXEGFNOLB-XUIBUIKDSA-N  
Z7P  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O"  
Z7P  SMILES            CACTVS                3.385  "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O"  
Z7P  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)C)O"  
Z7P  SMILES            "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(OC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)C)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
Z7P  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4S,5S,6R)-3,4-dihydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyloxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
Z7P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-methyl-5-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,4-bis(oxidanyl)oxan-2-yl] hydrogen 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
Z7P  "Create component"  2021-04-12  RCSB  
Z7P  "Initial release"   2021-04-28  RCSB  
##
