data_YG
#

_chem_comp.id                                   YG
_chem_comp.name                                 WYBUTOSINE
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C21 H29 N6 O12 P"
_chem_comp.mon_nstd_parent_comp_id              G
_chem_comp.pdbx_synonyms                        
;Y-BASE; 1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC
ACID,4,9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL-9-OXO-METHYL ESTER
;

_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                       588.462
_chem_comp.one_letter_code                      G
_chem_comp.three_letter_code                    YG
_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       1EVV
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
YG  N1      N1    N  0  1  Y  N  N  44.744  -13.942   1.252  -0.938  -0.917   1.913  N1      YG   1  
YG  N2      N2    N  0  1  Y  N  N  44.558  -15.668   2.736  -2.990  -1.594   1.713  N2      YG   2  
YG  C2      C2    C  0  1  Y  N  N  43.937  -14.598   2.123  -1.962  -1.130   1.036  C2      YG   3  
YG  N3      N3    N  0  1  N  N  N  42.650  -14.255   2.388  -1.803  -0.859  -0.308  N3      YG   4  
YG  C3      C3    C  0  1  N  N  N  41.796  -15.012   3.368  -2.910  -1.093  -1.238  C3      YG   5  
YG  C4      C4    C  0  1  Y  N  N  42.253  -13.151   1.661  -0.607  -0.372  -0.773  C4      YG   6  
YG  C5      C5    C  0  1  Y  N  N  42.998  -12.415   0.752   0.438  -0.153   0.115  C5      YG   7  
YG  C6      C6    C  0  1  N  N  N  44.362  -12.803   0.487   0.248  -0.439   1.490  C6      YG   8  
YG  O6      O6    O  0  1  N  N  N  45.175  -12.285  -0.291   1.152  -0.255   2.284  O6      YG   9  
YG  N7      N7    N  0  1  Y  N  N  42.247  -11.366   0.234   1.485   0.324  -0.605  N7      YG  10  
YG  C8      C8    C  0  1  Y  N  N  41.083  -11.473   0.822   1.140   0.406  -1.856  C8      YG  11  
YG  N9      N9    N  0  1  Y  N  N  41.016  -12.527   1.705  -0.148  -0.015  -2.004  N9      YG  12  
YG  C10     C10   C  0  1  N  N  N  46.936  -16.678   2.574  -3.564  -2.187   4.112  C10     YG  13  
YG  C11     C11   C  0  1  Y  N  N  45.847  -15.692   2.226  -2.661  -1.695   3.010  C11     YG  14  
YG  C12     C12   C  0  1  Y  N  N  45.937  -14.639   1.330  -1.393  -1.276   3.163  C12     YG  15  
YG  C13     C13   C  0  1  N  N  N  47.181  -14.328   0.528  -0.617  -1.215   4.452  C13     YG  16  
YG  C14     C14   C  0  1  N  N  N  47.458  -15.392  -0.513  -0.819   0.153   5.106  C14     YG  17  
YG  C15     C15   C  0  1  N  N  R  48.845  -16.050  -0.454  -0.031   0.214   6.416  C15     YG  18  
YG  C16     C16   C  0  1  N  N  N  49.306  -16.490  -1.848  -0.230   1.562   7.059  C16     YG  19  
YG  O17     O17   O  0  1  N  N  N  49.152  -15.747  -2.819  -1.141   1.732   7.835  O17     YG  20  
YG  O18     O18   O  0  1  N  N  N  49.854  -17.722  -1.968   0.603   2.573   6.771  O18     YG  21  
YG  C19     C19   C  0  1  N  N  N  51.257  -17.925  -2.286   0.411   3.872   7.391  C19     YG  22  
YG  N20     N20   N  0  1  N  N  N  48.845  -17.176   0.482   1.393   0.011   6.138  N20     YG  23  
YG  C21     C21   C  0  1  N  N  N  49.763  -17.348   1.434   2.184  -0.564   7.064  C21     YG  24  
YG  O22     O22   O  0  1  N  N  N  50.637  -16.503   1.658   1.717  -0.915   8.129  O22     YG  25  
YG  O23     O23   O  0  1  N  N  N  49.718  -18.480   2.178   3.493  -0.750   6.809  O23     YG  26  
YG  C24     C24   C  0  1  N  N  N  50.557  -18.696   3.340   4.346  -1.371   7.807  C24     YG  27  
YG  "C1'"   C1*   C  0  1  N  N  R  39.868  -12.898   2.535  -0.901  -0.074  -3.259  "C1'"   YG  28  
YG  "C2'"   C2*   C  0  1  N  N  R  40.093  -12.669   4.036  -1.614   1.270  -3.523  "C2'"   YG  29  
YG  "O2'"   O2*   O  0  1  N  N  N  39.528  -13.723   4.791  -2.984   1.204  -3.121  "O2'"   YG  30  
YG  "C3'"   C3*   C  0  1  N  N  S  39.388  -11.338   4.253  -1.507   1.456  -5.054  "C3'"   YG  31  
YG  "O3'"   O3*   O  0  1  N  N  N  38.968  -11.194   5.600  -2.807   1.508  -5.645  "O3'"   YG  32  
YG  "C4'"   C4*   C  0  1  N  N  R  38.194  -11.472   3.333  -0.746   0.200  -5.533  "C4'"   YG  33  
YG  "O4'"   O4*   O  0  1  N  N  N  38.766  -12.092   2.154  -0.002  -0.243  -4.377  "O4'"   YG  34  
YG  "C5'"   C5*   C  0  1  N  N  N  37.541  -10.173   2.951   0.208   0.556  -6.675  "C5'"   YG  35  
YG  "O5'"   O5*   O  0  1  N  N  N  38.443   -9.380   2.192   0.953  -0.602  -7.053  "O5'"   YG  36  
YG  P       P     P  0  1  N  N  N  37.928   -8.086   1.424   1.930  -0.157  -8.252  P       YG  37  
YG  OP1     O1P   O  0  1  N  N  N  39.097   -7.469   0.736   2.833   0.915  -7.779  OP1     YG  38  
YG  OP2     O2P   O  0  1  N  N  N  37.108   -7.272   2.363   2.805  -1.422  -8.729  OP2     YG  39  
YG  OP3     O3P   O  0  1  N  Y  N  36.937   -8.673   0.301   1.052   0.384  -9.487  OP3     YG  40  
YG  H31     1H3   H  0  1  N  N  N  40.739  -14.730   3.585  -3.770  -1.478  -0.690  H31     YG  41  
YG  H32     2H3   H  0  1  N  N  N  41.802  -16.084   3.061  -3.179  -0.156  -1.725  H32     YG  42  
YG  H33     3H3   H  0  1  N  N  N  42.343  -15.040   4.339  -2.604  -1.819  -1.992  H33     YG  43  
YG  H8      H8    H  0  1  N  N  N  40.264  -10.766   0.602   1.777   0.755  -2.656  H8      YG  44  
YG  H101    1H10  H  0  0  N  N  N  47.972  -16.697   2.163  -3.452  -3.266   4.219  H101    YG  45  
YG  H102    2H10  H  0  0  N  N  N  47.041  -16.645   3.683  -3.294  -1.699   5.048  H102    YG  46  
YG  H103    3H10  H  0  0  N  N  N  46.509  -17.690   2.386  -4.600  -1.952   3.865  H103    YG  47  
YG  H131    1H13  H  0  0  N  N  N  47.124  -13.314   0.067   0.442  -1.366   4.246  H131    YG  48  
YG  H132    2H13  H  0  0  N  N  N  48.063  -14.169   1.191  -0.970  -1.995   5.126  H132    YG  49  
YG  H141    1H14  H  0  0  N  N  N  46.666  -16.175  -0.472  -1.879   0.303   5.312  H141    YG  50  
YG  H142    2H14  H  0  0  N  N  N  47.279  -14.978  -1.532  -0.466   0.933   4.432  H142    YG  51  
YG  H15     H15   H  0  1  N  N  N  49.572  -15.291  -0.081  -0.384  -0.565   7.090  H15     YG  52  
YG  H191    1H19  H  0  0  N  N  N  51.708  -18.939  -2.384   1.178   4.561   7.038  H191    YG  53  
YG  H192    2H19  H  0  0  N  N  N  51.472  -17.367  -3.227  -0.573   4.259   7.127  H192    YG  54  
YG  H193    3H19  H  0  0  N  N  N  51.857  -17.361  -1.534   0.483   3.772   8.474  H193    YG  55  
YG  HN2     HN2   H  0  1  N  N  N  48.137  -17.910   0.469   1.766   0.292   5.288  HN2     YG  56  
YG  H241    1H24  H  0  0  N  N  N  50.520  -19.627   3.952   5.364  -1.437   7.424  H241    YG  57  
YG  H242    2H24  H  0  0  N  N  N  51.614  -18.550   3.019   4.338  -0.770   8.716  H242    YG  58  
YG  H243    3H24  H  0  0  N  N  N  50.396  -17.836   4.031   3.976  -2.372   8.029  H243    YG  59  
YG  "H1'"   H1*   H  0  1  N  N  N  39.696  -13.988   2.375  -1.625  -0.888  -3.229  "H1'"   YG  60  
YG  "H2'"   H2*   H  0  1  N  N  N  41.161  -12.648   4.355  -1.103   2.080  -3.003  "H2'"   YG  61  
YG  "HO2'"  *HO2  H  0  0  N  N  N  39.667  -13.581   5.720  -3.388   2.048  -3.366  "HO2'"  YG  62  
YG  "H3'"   H3*   H  0  1  N  N  N  40.029  -10.449   4.047  -0.944   2.358  -5.292  "H3'"   YG  63  
YG  "HO3'"  *HO3  H  0  0  N  Y  N  38.527  -10.363   5.735  -3.234   2.309  -5.311  "HO3'"  YG  64  
YG  "H4'"   H4*   H  0  1  N  N  N  37.378  -12.043   3.833  -1.447  -0.570  -5.852  "H4'"   YG  65  
YG  "H5'"   1H5*  H  0  1  N  N  N  36.574  -10.332   2.418  -0.366   0.914  -7.530  "H5'"   YG  66  
YG  "H5''"  2H5*  H  0  0  N  N  N  37.149   -9.625   3.839   0.893   1.337  -6.346  "H5''"  YG  67  
YG  HOP2    2HOP  H  0  0  N  N  N  36.800   -6.499   1.904   3.375  -1.113  -9.446  HOP2    YG  68  
YG  HOP3    3HOP  H  0  0  N  N  N  36.629   -7.900  -0.157   0.479  -0.344  -9.764  HOP3    YG  69  
#   #
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
YG  N1     C2      SING  Y  N   1  
YG  N1     C6      SING  N  N   2  
YG  N1     C12     SING  Y  N   3  
YG  N2     C2      DOUB  Y  N   4  
YG  N2     C11     SING  Y  N   5  
YG  C2     N3      SING  N  N   6  
YG  N3     C3      SING  N  N   7  
YG  N3     C4      SING  N  N   8  
YG  C3     H31     SING  N  N   9  
YG  C3     H32     SING  N  N  10  
YG  C3     H33     SING  N  N  11  
YG  C4     C5      DOUB  Y  N  12  
YG  C4     N9      SING  Y  N  13  
YG  C5     C6      SING  N  N  14  
YG  C5     N7      SING  Y  N  15  
YG  C6     O6      DOUB  N  N  16  
YG  N7     C8      DOUB  Y  N  17  
YG  C8     N9      SING  Y  N  18  
YG  C8     H8      SING  N  N  19  
YG  N9     "C1'"   SING  N  N  20  
YG  C10    C11     SING  N  N  21  
YG  C10    H101    SING  N  N  22  
YG  C10    H102    SING  N  N  23  
YG  C10    H103    SING  N  N  24  
YG  C11    C12     DOUB  Y  N  25  
YG  C12    C13     SING  N  N  26  
YG  C13    C14     SING  N  N  27  
YG  C13    H131    SING  N  N  28  
YG  C13    H132    SING  N  N  29  
YG  C14    C15     SING  N  N  30  
YG  C14    H141    SING  N  N  31  
YG  C14    H142    SING  N  N  32  
YG  C15    C16     SING  N  N  33  
YG  C15    N20     SING  N  N  34  
YG  C15    H15     SING  N  N  35  
YG  C16    O17     DOUB  N  N  36  
YG  C16    O18     SING  N  N  37  
YG  O18    C19     SING  N  N  38  
YG  C19    H191    SING  N  N  39  
YG  C19    H192    SING  N  N  40  
YG  C19    H193    SING  N  N  41  
YG  N20    C21     SING  N  N  42  
YG  N20    HN2     SING  N  N  43  
YG  C21    O22     DOUB  N  N  44  
YG  C21    O23     SING  N  N  45  
YG  O23    C24     SING  N  N  46  
YG  C24    H241    SING  N  N  47  
YG  C24    H242    SING  N  N  48  
YG  C24    H243    SING  N  N  49  
YG  "C1'"  "C2'"   SING  N  N  50  
YG  "C1'"  "O4'"   SING  N  N  51  
YG  "C1'"  "H1'"   SING  N  N  52  
YG  "C2'"  "O2'"   SING  N  N  53  
YG  "C2'"  "C3'"   SING  N  N  54  
YG  "C2'"  "H2'"   SING  N  N  55  
YG  "O2'"  "HO2'"  SING  N  N  56  
YG  "C3'"  "O3'"   SING  N  N  57  
YG  "C3'"  "C4'"   SING  N  N  58  
YG  "C3'"  "H3'"   SING  N  N  59  
YG  "O3'"  "HO3'"  SING  N  N  60  
YG  "C4'"  "O4'"   SING  N  N  61  
YG  "C4'"  "C5'"   SING  N  N  62  
YG  "C4'"  "H4'"   SING  N  N  63  
YG  "C5'"  "O5'"   SING  N  N  64  
YG  "C5'"  "H5'"   SING  N  N  65  
YG  "C5'"  "H5''"  SING  N  N  66  
YG  "O5'"  P       SING  N  N  67  
YG  P      OP1     DOUB  N  N  68  
YG  P      OP2     SING  N  N  69  
YG  P      OP3     SING  N  N  70  
YG  OP2    HOP2    SING  N  N  71  
YG  OP3    HOP3    SING  N  N  72  
#   #
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
YG  SMILES            ACDLabs               10.04  "O=C(OC)C(NC(=O)OC)CCc3c(nc4N(c1c(ncn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)n34)C)C"  
YG  SMILES_CANONICAL  CACTVS                3.341  "COC(=O)N[C@H](CCc1n2C(=O)c3ncn([C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O)c3N(C)c2nc1C)C(=O)OC"  
YG  SMILES            CACTVS                3.341  "COC(=O)N[CH](CCc1n2C(=O)c3ncn([CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O)c3N(C)c2nc1C)C(=O)OC"  
YG  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "Cc1c(n2c(n1)N(c3c(ncn3[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)C2=O)C)CC[C@H](C(=O)OC)NC(=O)OC"  
YG  SMILES            "OpenEye OEToolkits"  1.5.0  "Cc1c(n2c(n1)N(c3c(ncn3C4C(C(C(O4)COP(=O)(O)O)O)O)C2=O)C)CCC(C(=O)OC)NC(=O)OC"  
YG  InChI             InChI                 1.03   "InChI=1S/C21H29N6O12P/c1-9-11(6-5-10(19(31)36-3)24-21(32)37-4)27-17(30)13-16(25(2)20(27)23-9)26(8-22-13)18-15(29)14(28)12(39-18)7-38-40(33,34)35/h8,10,12,14-15,18,28-29H,5-7H2,1-4H3,(H,24,32)(H2,33,34,35)/t10-,12-,14-,15-,18-/m1/s1"  
YG  InChIKey          InChI                 1.03   WOMRPCAFQVCGCI-DPHITLOKSA-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
YG  "SYSTEMATIC NAME"  ACDLabs               10.04  "7-{(3R)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,6-dimethyl-3-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one"  
YG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "methyl (2R)-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-4,6-dimethyl-9-oxo-imidazo[3,2-a]purin-7-yl]-2-(methoxycarbonylamino)butanoate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YG  "Create component"   1999-07-08  PDBJ  
YG  "Modify descriptor"  2011-06-04  RCSB  
YG  "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  YG  Y-BASE                                                                                                                    ?  ?  
2  YG  "1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC ACID,4,9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL-9-OXO-METHYL ESTER"  ?  ?  
##
