data_VPA # _chem_comp.id VPA _chem_comp.name "2-phenyl-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)ethylamidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H28 N2 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]e thanimidamide ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-31 _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 428.434 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VPA _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 3WQ5 _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 VPA C1 C1 C 0 1 N N N -29.216 12.631 -21.601 -3.257 -0.119 0.411 C1 VPA 1 VPA C2 C2 C 0 1 N N N -29.025 12.387 -20.099 -4.243 -0.915 1.227 C2 VPA 2 VPA N2 N2 N 0 1 N N N -30.400 12.493 -22.178 -2.914 -0.528 -0.767 N2 VPA 3 VPA C3 C3 C 0 1 Y N N -29.867 11.204 -19.567 -4.673 -2.131 0.448 C3 VPA 4 VPA C4 C4 C 0 1 Y N N -30.160 11.154 -18.206 -3.969 -3.315 0.571 C4 VPA 5 VPA C5 C5 C 0 1 Y N N -30.912 10.109 -17.676 -4.364 -4.431 -0.143 C5 VPA 6 VPA C6 C6 C 0 1 Y N N -31.378 9.098 -18.507 -5.463 -4.363 -0.980 C6 VPA 7 VPA C8 C8 C 0 1 Y N N -30.336 10.180 -20.392 -5.775 -2.065 -0.384 C8 VPA 8 VPA C7 C7 C 0 1 Y N N -31.093 9.137 -19.867 -6.166 -3.180 -1.102 C7 VPA 9 VPA N1 N1 N 0 1 N N N -28.186 13.046 -22.322 -2.728 1.040 0.915 N1 VPA 10 VPA "C1'" "C1'" C 0 1 N N R -28.304 13.275 -23.775 -1.769 1.813 0.122 "C1'" VPA 11 VPA "O5'" "O5'" O 0 1 N N N -29.705 13.511 -24.084 -0.439 1.447 0.493 "O5'" VPA 12 VPA "C2'" "C2'" C 0 1 N N R -27.614 12.067 -24.441 -1.978 3.307 0.383 "C2'" VPA 13 VPA "O2'" "O2'" O 0 1 N N N -26.216 12.348 -24.587 -3.289 3.687 -0.040 "O2'" VPA 14 VPA "C3'" "C3'" C 0 1 N N S -28.232 11.696 -25.793 -0.933 4.106 -0.403 "C3'" VPA 15 VPA "O3'" "O3'" O 0 1 N N N -27.812 10.390 -26.205 -1.074 5.497 -0.108 "O3'" VPA 16 VPA "C4'" "C4'" C 0 1 N N S -29.741 11.719 -25.643 0.466 3.634 0.004 "C4'" VPA 17 VPA "O4'" "O4'" O 0 1 N N N -30.362 11.208 -26.818 1.447 4.321 -0.775 "O4'" VPA 18 VPA "C5'" "C5'" C 0 1 N N R -30.183 13.147 -25.380 0.580 2.127 -0.243 "C5'" VPA 19 VPA "C6'" "C6'" C 0 1 N N N -31.689 13.203 -25.267 1.955 1.638 0.218 "C6'" VPA 20 VPA "O6'" "O6'" O 0 1 N N N -31.955 12.380 -24.116 2.106 0.257 -0.119 "O6'" VPA 21 VPA C1A C1A C 0 1 N N S -33.354 12.135 -23.952 3.362 -0.302 0.270 C1A VPA 22 VPA O5A O5A O 0 1 N N N -33.847 13.002 -22.899 4.412 0.329 -0.467 O5A VPA 23 VPA C5A C5A C 0 1 N N N -35.248 12.780 -22.631 5.721 -0.140 -0.135 C5A VPA 24 VPA C4A C4A C 0 1 N N R -35.453 11.337 -22.171 5.819 -1.636 -0.445 C4A VPA 25 VPA O4A O4A O 0 1 N N N -36.826 11.107 -21.849 7.108 -2.120 -0.061 O4A VPA 26 VPA C3A C3A C 0 1 N N S -35.011 10.402 -23.289 4.736 -2.384 0.338 C3A VPA 27 VPA O3A O3A O 0 1 N N N -35.204 9.047 -22.896 4.773 -3.772 -0.001 O3A VPA 28 VPA C2A C2A C 0 1 N N R -33.539 10.663 -23.575 3.366 -1.804 -0.024 C2A VPA 29 VPA O2A O2A O 0 1 N N N -33.066 9.809 -24.625 2.354 -2.446 0.755 O2A VPA 30 VPA H1 H1 H 0 1 N N N -27.962 12.173 -19.911 -3.774 -1.227 2.160 H1 VPA 31 VPA H2 H2 H 0 1 N N N -29.318 13.298 -19.556 -5.114 -0.298 1.447 H2 VPA 32 VPA H3 H3 H 0 1 N N N -31.106 12.222 -21.524 -3.291 -1.347 -1.126 H3 VPA 33 VPA H4 H4 H 0 1 N N N -29.799 11.936 -17.554 -3.111 -3.368 1.224 H4 VPA 34 VPA H5 H5 H 0 1 N N N -31.133 10.084 -16.619 -3.814 -5.355 -0.048 H5 VPA 35 VPA H6 H6 H 0 1 N N N -31.959 8.285 -18.098 -5.771 -5.235 -1.538 H6 VPA 36 VPA H7 H7 H 0 1 N N N -30.109 10.197 -21.448 -6.325 -1.141 -0.480 H7 VPA 37 VPA H8 H8 H 0 1 N N N -31.460 8.357 -20.517 -7.027 -3.128 -1.752 H8 VPA 38 VPA H9 H9 H 0 1 N N N -27.308 13.208 -21.872 -2.988 1.348 1.797 H9 VPA 39 VPA H10 H10 H 0 1 N N N -27.727 14.175 -24.035 -1.921 1.604 -0.937 H10 VPA 40 VPA H11 H11 H 0 1 N N N -27.736 11.204 -23.770 -1.866 3.510 1.448 H11 VPA 41 VPA H12 H12 H 0 1 N N N -25.848 12.576 -23.741 -4.001 3.216 0.414 H12 VPA 42 VPA H13 H13 H 0 1 N N N -27.933 12.446 -26.540 -1.077 3.942 -1.471 H13 VPA 43 VPA H14 H14 H 0 1 N N N -26.867 10.376 -26.299 -1.938 5.863 -0.340 H14 VPA 44 VPA H15 H15 H 0 1 N N N -30.017 11.101 -24.776 0.628 3.843 1.062 H15 VPA 45 VPA H16 H16 H 0 1 N N N -31.306 11.228 -26.712 1.429 5.283 -0.672 H16 VPA 46 VPA H17 H17 H 0 1 N N N -29.819 13.824 -26.167 0.459 1.923 -1.306 H17 VPA 47 VPA H18 H18 H 0 1 N N N -32.036 14.234 -25.105 2.732 2.219 -0.278 H18 VPA 48 VPA H19 H19 H 0 1 N N N -32.169 12.792 -26.167 2.042 1.760 1.297 H19 VPA 49 VPA H20 H20 H 0 1 N N N -33.892 12.335 -24.890 3.518 -0.140 1.336 H20 VPA 50 VPA H21 H21 H 0 1 N N N -35.584 13.468 -21.842 6.461 0.403 -0.723 H21 VPA 51 VPA H22 H22 H 0 1 N N N -35.830 12.960 -23.547 5.908 0.024 0.927 H22 VPA 52 VPA H23 H23 H 0 1 N N N -34.823 11.155 -21.288 5.674 -1.797 -1.513 H23 VPA 53 VPA H24 H24 H 0 1 N N N -37.091 11.695 -21.151 7.843 -1.686 -0.515 H24 VPA 54 VPA H25 H25 H 0 1 N N N -35.596 10.625 -24.193 4.912 -2.266 1.408 H25 VPA 55 VPA H26 H26 H 0 1 N N N -36.125 8.896 -22.720 5.616 -4.203 0.195 H26 VPA 56 VPA H27 H27 H 0 1 N N N -32.967 10.468 -22.656 3.170 -1.968 -1.084 H27 VPA 57 VPA H28 H28 H 0 1 N N N -33.188 8.901 -24.374 1.460 -2.123 0.580 H28 VPA 58 # # 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 VPA "O4'" "C4'" SING N N 1 VPA "O3'" "C3'" SING N N 2 VPA "C3'" "C4'" SING N N 3 VPA "C3'" "C2'" SING N N 4 VPA "C4'" "C5'" SING N N 5 VPA "C5'" "C6'" SING N N 6 VPA "C5'" "O5'" SING N N 7 VPA "C6'" "O6'" SING N N 8 VPA O2A C2A SING N N 9 VPA "O2'" "C2'" SING N N 10 VPA "C2'" "C1'" SING N N 11 VPA "O6'" C1A SING N N 12 VPA "O5'" "C1'" SING N N 13 VPA C1A C2A SING N N 14 VPA C1A O5A SING N N 15 VPA "C1'" N1 SING N N 16 VPA C2A C3A SING N N 17 VPA C3A O3A SING N N 18 VPA C3A C4A SING N N 19 VPA O5A C5A SING N N 20 VPA C5A C4A SING N N 21 VPA N1 C1 SING N N 22 VPA N2 C1 DOUB N N 23 VPA C4A O4A SING N N 24 VPA C1 C2 SING N N 25 VPA C8 C7 DOUB Y N 26 VPA C8 C3 SING Y N 27 VPA C2 C3 SING N N 28 VPA C7 C6 SING Y N 29 VPA C3 C4 DOUB Y N 30 VPA C6 C5 DOUB Y N 31 VPA C4 C5 SING Y N 32 VPA C2 H1 SING N N 33 VPA C2 H2 SING N N 34 VPA N2 H3 SING N N 35 VPA C4 H4 SING N N 36 VPA C5 H5 SING N N 37 VPA C6 H6 SING N N 38 VPA C8 H7 SING N N 39 VPA C7 H8 SING N N 40 VPA N1 H9 SING N N 41 VPA "C1'" H10 SING N N 42 VPA "C2'" H11 SING N N 43 VPA "O2'" H12 SING N N 44 VPA "C3'" H13 SING N N 45 VPA "O3'" H14 SING N N 46 VPA "C4'" H15 SING N N 47 VPA "O4'" H16 SING N N 48 VPA "C5'" H17 SING N N 49 VPA "C6'" H18 SING N N 50 VPA "C6'" H19 SING N N 51 VPA C1A H20 SING N N 52 VPA C5A H21 SING N N 53 VPA C5A H22 SING N N 54 VPA C4A H23 SING N N 55 VPA O4A H24 SING N N 56 VPA C3A H25 SING N N 57 VPA O3A H26 SING N N 58 VPA C2A H27 SING N N 59 VPA O2A H28 SING N N 60 # # 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 VPA SMILES ACDLabs 12.01 "O(CC2OC(NC(=[N@H])Cc1ccccc1)C(O)C(O)C2O)C3OCC(O)C(O)C3O" VPA InChI InChI 1.03 "InChI=1S/C19H28N2O9/c20-12(6-9-4-2-1-3-5-9)21-18-16(26)15(25)14(24)11(30-18)8-29-19-17(27)13(23)10(22)7-28-19/h1-5,10-11,13-19,22-27H,6-8H2,(H2,20,21)/t10-,11-,13+,14-,15+,16-,17-,18-,19+/m1/s1" VPA InChIKey InChI 1.03 SKGTWJNDCFMXKU-GZDQRYBESA-N VPA SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)Cc3ccccc3)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O" VPA SMILES CACTVS 3.385 "O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)Cc3ccccc3)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O" VPA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C(\Cc1ccccc1)/N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)O" VPA SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CC(=N)NC2C(C(C(C(O2)COC3C(C(C(CO3)O)O)O)O)O)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 VPA "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(1E)-2-phenylethanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine" VPA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]ethanimidamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VPA "Create component" 2014-01-31 PDBJ VPA "Modify name" 2014-02-18 PDBJ VPA "Modify synonyms" 2014-02-18 PDBJ VPA "Initial release" 2014-04-23 RCSB VPA "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VPA _pdbx_chem_comp_synonyms.name "2-phenyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]ethanimidamide" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##