data_VGP
#

_chem_comp.id                                   VGP
_chem_comp.name                                 "(1R)-1,4-anhydro-6-deoxy-1-[(6R)-8-ethenyl-1,6-dihydroxy-10,12-dimethoxy-6H-dibenzo[c,h]chromen-4-yl]-D-galactitol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C27 H28 O9"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "pregilvocarcin V"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2010-11-30
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       496.506
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VGP
_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       3PQB
_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
VGP  C     C     C  0  1  N  N  N  29.315   -8.052   95.070   5.886   1.205   0.677  C     VGP   1  
VGP  O     O     O  0  1  N  N  N  25.090   -4.359  106.675  -6.123  -0.817  -0.484  O     VGP   2  
VGP  C01   C01   C  0  1  Y  N  N  23.913   -7.930  101.881  -2.532   3.286   0.107  C01   VGP   3  
VGP  O01   O01   O  0  1  N  N  N  28.332   -5.825  100.965  -0.003  -1.054   0.335  O01   VGP   4  
VGP  C02   C02   C  0  1  Y  N  N  24.747   -7.099  102.613  -2.919   1.957   0.255  C02   VGP   5  
VGP  O02   O02   O  0  1  N  N  N  23.462   -9.095   99.912  -0.839   4.923  -0.170  O02   VGP   6  
VGP  C03   C03   C  0  1  Y  N  N  25.938   -6.657  102.076  -1.995   0.957   0.281  C03   VGP   7  
VGP  O03   O03   O  0  1  N  N  N  25.084   -9.085   98.015   1.535   4.216  -0.270  O03   VGP   8  
VGP  C04   C04   C  0  1  Y  N  N  26.345   -7.043  100.780  -0.628   1.261   0.156  C04   VGP   9  
VGP  O04   O04   O  0  1  N  N  N  28.912   -7.688   96.319   4.484   1.025   0.470  O04   VGP  10  
VGP  C05   C05   C  0  1  Y  N  N  25.517   -7.875  100.044  -0.225   2.611   0.004  C05   VGP  11  
VGP  O05   O05   O  0  1  N  N  N  30.445   -5.159  101.522   0.488  -1.981  -1.747  O05   VGP  12  
VGP  C06   C06   C  0  1  Y  N  N  24.302   -8.301  100.604  -1.204   3.623  -0.025  C06   VGP  13  
VGP  O06   O06   O  0  1  N  N  N  26.053   -5.304  103.958  -3.731  -0.538   1.080  O06   VGP  14  
VGP  C07   C07   C  0  1  Y  N  N  27.547   -6.619  100.208   0.347   0.248   0.183  C07   VGP  15  
VGP  O07   O07   O  0  1  N  N  N  28.436   -6.871  105.860  -2.999  -3.503  -0.441  O07   VGP  16  
VGP  C08   C08   C  0  1  Y  N  N  27.935   -7.002   98.930   1.690   0.591   0.055  C08   VGP  17  
VGP  O08   O08   O  0  1  N  N  N  27.770   -7.979  103.160  -3.268  -0.194  -1.851  O08   VGP  18  
VGP  C09   C09   C  0  1  Y  N  N  27.096   -7.832   98.213   2.077   1.928  -0.095  C09   VGP  19  
VGP  C10   C10   C  0  1  Y  N  N  25.905   -8.256   98.756   1.144   2.923  -0.122  C10   VGP  20  
VGP  C11   C11   C  0  1  N  N  R  29.512   -5.295  100.552   0.766  -2.046  -0.346  C11   VGP  21  
VGP  C12   C12   C  0  1  Y  N  N  29.954   -5.705   99.200   2.236  -1.810  -0.116  C12   VGP  22  
VGP  C13   C13   C  0  1  Y  N  N  29.169   -6.528   98.404   2.690  -0.501   0.078  C13   VGP  23  
VGP  C14   C14   C  0  1  Y  N  N  31.157   -5.218   98.764   3.127  -2.856  -0.094  C14   VGP  24  
VGP  C15   C15   C  0  1  Y  N  N  31.621   -5.552   97.514   4.487  -2.609   0.117  C15   VGP  25  
VGP  C16   C16   C  0  1  Y  N  N  30.874   -6.383   96.695   4.943  -1.302   0.306  C16   VGP  26  
VGP  C17   C17   C  0  1  Y  N  N  29.647   -6.875   97.139   4.046  -0.249   0.287  C17   VGP  27  
VGP  C18   C18   C  0  1  N  N  N  32.948   -4.994   97.065   5.444  -3.733   0.140  C18   VGP  28  
VGP  C19   C19   C  0  1  N  N  N  33.315   -3.592   97.386   6.735  -3.501   0.340  C19   VGP  29  
VGP  C20   C20   C  0  1  N  N  R  27.756   -6.718  103.664  -2.684  -1.129  -0.941  C20   VGP  30  
VGP  C21   C21   C  0  1  N  N  R  26.817   -5.801  102.950  -2.438  -0.475   0.442  C21   VGP  31  
VGP  C22   C22   C  0  1  N  N  R  27.339   -6.760  105.065  -3.684  -2.258  -0.592  C22   VGP  32  
VGP  C23   C23   C  0  1  N  N  S  26.561   -5.507  105.222  -4.300  -1.816   0.749  C23   VGP  33  
VGP  C24   C24   C  0  1  N  N  R  25.351   -5.565  106.116  -5.818  -1.688   0.607  C24   VGP  34  
VGP  C25   C25   C  0  1  N  N  N  25.530   -6.519  107.203  -6.405  -1.113   1.898  C25   VGP  35  
VGP  C26   C26   C  0  1  N  N  N  25.626   -9.762   96.947   2.938   4.460  -0.392  C26   VGP  36  
VGP  H     H     H  0  1  N  N  N  28.556   -8.705   94.615   6.100   2.266   0.809  H     VGP  37  
VGP  HA    HA    H  0  1  N  N  N  29.444   -7.153   94.450   6.194   0.658   1.568  HA    VGP  38  
VGP  HB    HB    H  0  1  N  N  N  30.271   -8.592   95.136   6.432   0.829  -0.188  HB    VGP  39  
VGP  HO    HO    H  0  1  N  N  N  24.323   -4.427  107.232  -5.770   0.077  -0.384  HO    VGP  40  
VGP  H01   H01   H  0  1  N  N  N  22.980   -8.281  102.297  -3.284   4.062   0.090  H01   VGP  41  
VGP  H02   H02   H  0  1  N  N  N  24.462   -6.796  103.610  -3.967   1.715   0.353  H02   VGP  42  
VGP  HO02  HO02  H  0  0  N  N  N  22.695   -9.283  100.441  -0.793   5.218  -1.090  HO02  VGP  43  
VGP  HO07  HO07  H  0  0  N  N  N  28.166   -6.898  106.771  -2.543  -3.801  -1.240  HO07  VGP  44  
VGP  HO08  HO08  H  0  0  N  N  N  28.041   -7.954  102.250  -3.523  -0.579  -2.700  HO08  VGP  45  
VGP  H09   H09   H  0  1  N  N  N  27.376   -8.150   97.220   3.124   2.173  -0.191  H09   VGP  46  
VGP  H14   H14   H  0  1  N  N  N  31.741   -4.572   99.402   2.778  -3.867  -0.241  H14   VGP  47  
VGP  H16   H16   H  0  1  N  N  N  31.241   -6.649   95.715   5.994  -1.115   0.467  H16   VGP  48  
VGP  H18   H18   H  0  1  N  N  N  33.633   -5.616   96.508   5.094  -4.744  -0.006  H18   VGP  49  
VGP  H19   H19   H  0  1  N  N  N  34.266   -3.195   97.063   7.435  -4.323   0.357  H19   VGP  50  
VGP  H19A  H19A  H  0  0  N  N  N  32.631   -2.969   97.943   7.085  -2.490   0.486  H19A  VGP  51  
VGP  H20   H20   H  0  1  N  N  N  28.778   -6.329  103.541  -1.760  -1.540  -1.348  H20   VGP  52  
VGP  H21   H21   H  0  1  N  N  N  27.308   -5.026  102.343  -1.701  -1.041   1.012  H21   VGP  53  
VGP  H22   H22   H  0  1  N  N  N  26.721   -7.622  105.356  -4.453  -2.338  -1.360  H22   VGP  54  
VGP  H23   H23   H  0  1  N  N  N  27.227   -4.751  105.664  -4.058  -2.542   1.526  H23   VGP  55  
VGP  H24   H24   H  0  1  N  N  N  24.515   -5.877  105.473  -6.249  -2.672   0.418  H24   VGP  56  
VGP  H25   H25   H  0  1  N  N  N  24.628   -6.533  107.832  -5.974  -0.130   2.086  H25   VGP  57  
VGP  H25A  H25A  H  0  0  N  N  N  25.701   -7.522  106.786  -7.486  -1.023   1.796  H25A  VGP  58  
VGP  H25B  H25B  H  0  0  N  N  N  26.397   -6.222  107.812  -6.172  -1.778   2.730  H25B  VGP  59  
VGP  H26   H26   H  0  1  N  N  N  24.848  -10.373   96.467   3.112   5.530  -0.504  H26   VGP  60  
VGP  H26A  H26A  H  0  0  N  N  N  26.026   -9.040   96.220   3.448   4.101   0.501  H26A  VGP  61  
VGP  H26B  H26B  H  0  0  N  N  N  26.438  -10.414   97.301   3.323   3.936  -1.267  H26B  VGP  62  
VGP  H27   H27   H  0  1  N  N  N  31.235   -4.784  101.152  -0.405  -2.265  -1.984  H27   VGP  63  
VGP  H28   H28   H  0  1  N  N  N  29.289   -4.237  100.351   0.497  -3.033   0.030  H28   VGP  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
VGP  C    O04   SING  N  N   1  
VGP  C    H     SING  N  N   2  
VGP  C    HA    SING  N  N   3  
VGP  C    HB    SING  N  N   4  
VGP  O    HO    SING  N  N   5  
VGP  C01  C02   SING  Y  N   6  
VGP  C01  H01   SING  N  N   7  
VGP  C02  H02   SING  N  N   8  
VGP  O02  C06   SING  N  N   9  
VGP  O02  HO02  SING  N  N  10  
VGP  C03  C02   DOUB  Y  N  11  
VGP  C03  C21   SING  N  N  12  
VGP  O03  C10   SING  N  N  13  
VGP  C04  C03   SING  Y  N  14  
VGP  O04  C17   SING  N  N  15  
VGP  C05  C04   SING  Y  N  16  
VGP  C05  C06   SING  Y  N  17  
VGP  C06  C01   DOUB  Y  N  18  
VGP  O06  C23   SING  N  N  19  
VGP  C07  O01   SING  N  N  20  
VGP  C07  C04   DOUB  Y  N  21  
VGP  O07  HO07  SING  N  N  22  
VGP  C08  C07   SING  Y  N  23  
VGP  O08  C20   SING  N  N  24  
VGP  O08  HO08  SING  N  N  25  
VGP  C09  C08   DOUB  Y  N  26  
VGP  C09  C10   SING  Y  N  27  
VGP  C09  H09   SING  N  N  28  
VGP  C10  C05   DOUB  Y  N  29  
VGP  C11  O01   SING  N  N  30  
VGP  C11  O05   SING  N  N  31  
VGP  C12  C11   SING  N  N  32  
VGP  C13  C08   SING  Y  N  33  
VGP  C13  C12   DOUB  Y  N  34  
VGP  C14  C12   SING  Y  N  35  
VGP  C14  H14   SING  N  N  36  
VGP  C15  C14   DOUB  Y  N  37  
VGP  C16  C15   SING  Y  N  38  
VGP  C16  C17   DOUB  Y  N  39  
VGP  C16  H16   SING  N  N  40  
VGP  C17  C13   SING  Y  N  41  
VGP  C18  C15   SING  N  N  42  
VGP  C18  C19   DOUB  N  N  43  
VGP  C18  H18   SING  N  N  44  
VGP  C19  H19   SING  N  N  45  
VGP  C19  H19A  SING  N  N  46  
VGP  C20  C22   SING  N  N  47  
VGP  C20  H20   SING  N  N  48  
VGP  C21  O06   SING  N  N  49  
VGP  C21  C20   SING  N  N  50  
VGP  C21  H21   SING  N  N  51  
VGP  C22  O07   SING  N  N  52  
VGP  C22  C23   SING  N  N  53  
VGP  C22  H22   SING  N  N  54  
VGP  C23  C24   SING  N  N  55  
VGP  C23  H23   SING  N  N  56  
VGP  C24  O     SING  N  N  57  
VGP  C24  C25   SING  N  N  58  
VGP  C24  H24   SING  N  N  59  
VGP  C25  H25   SING  N  N  60  
VGP  C25  H25A  SING  N  N  61  
VGP  C25  H25B  SING  N  N  62  
VGP  C26  O03   SING  N  N  63  
VGP  C26  H26   SING  N  N  64  
VGP  C26  H26A  SING  N  N  65  
VGP  C26  H26B  SING  N  N  66  
VGP  O05  H27   SING  N  N  67  
VGP  C11  H28   SING  N  N  68  
#   #
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
VGP  SMILES            ACDLabs               12.01  "OC1C(OC(C(O)C)C1O)c5c4c3OC(O)c2cc(\C=C)cc(OC)c2c3cc(OC)c4c(O)cc5"  
VGP  SMILES_CANONICAL  CACTVS                3.370  "COc1cc(C=C)cc2[C@H](O)Oc3c(cc(OC)c4c(O)ccc([C@H]5O[C@@H]([C@@H](C)O)[C@H](O)[C@H]5O)c34)c12"  
VGP  SMILES            CACTVS                3.370  "COc1cc(C=C)cc2[CH](O)Oc3c(cc(OC)c4c(O)ccc([CH]5O[CH]([CH](C)O)[CH](O)[CH]5O)c34)c12"  
VGP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C[C@H]([C@H]1[C@@H]([C@H]([C@H](O1)c2ccc(c3c2c4c(cc3OC)-c5c(cc(cc5OC)C=C)[C@@H](O4)O)O)O)O)O"  
VGP  SMILES            "OpenEye OEToolkits"  1.7.0  "CC(C1C(C(C(O1)c2ccc(c3c2c4c(cc3OC)-c5c(cc(cc5OC)C=C)C(O4)O)O)O)O)O"  
VGP  InChI             InChI                 1.03   "InChI=1S/C27H28O9/c1-5-12-8-15-19(17(9-12)33-3)14-10-18(34-4)21-16(29)7-6-13(20(21)25(14)36-27(15)32)26-23(31)22(30)24(35-26)11(2)28/h5-11,22-24,26-32H,1H2,2-4H3/t11-,22-,23-,24+,26-,27-/m1/s1"  
VGP  InChIKey          InChI                 1.03   YVGUIYUDGGDTSX-ZDRXMRRKSA-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
VGP  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R)-1,4-anhydro-6-deoxy-1-[(6R)-8-ethenyl-1,6-dihydroxy-10,12-dimethoxy-6H-dibenzo[c,h]chromen-4-yl]-D-galactitol"  
VGP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "(6R)-4-[(2R,3R,4R,5S)-3,4-dihydroxy-5-[(1R)-1-hydroxyethyl]oxolan-2-yl]-8-ethenyl-10,12-dimethoxy-6H-naphtho[1,2-c]isochromene-1,6-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VGP  "Create component"      2010-11-30  RCSB  
VGP  "Modify aromatic_flag"  2011-06-04  RCSB  
VGP  "Modify descriptor"     2011-06-04  RCSB  
VGP  "Modify synonyms"       2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VGP
_pdbx_chem_comp_synonyms.name        "pregilvocarcin V"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
