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 ? ##