data_ZPA # _chem_comp.id ZPA _chem_comp.name "4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H37 N3 O11 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2 S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide ; _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 599.650 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZPA _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 3WQ6 _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 ZPA C13 C13 C 0 1 Y N N -1.323 31.563 18.016 8.994 1.008 -1.413 C13 ZPA 1 ZPA C14 C14 C 0 1 Y N N -0.340 30.864 18.711 9.853 0.925 -2.493 C14 ZPA 2 ZPA C15 C15 C 0 1 Y N N -0.452 30.675 20.084 10.979 0.126 -2.421 C15 ZPA 3 ZPA C16 C16 C 0 1 Y N N -1.554 31.184 20.764 11.245 -0.591 -1.269 C16 ZPA 4 ZPA C17 C17 C 0 1 Y N N -2.529 31.890 20.066 10.385 -0.509 -0.189 C17 ZPA 5 ZPA C12 C12 C 0 1 Y N N -2.416 32.093 18.692 9.260 0.290 -0.262 C12 ZPA 6 ZPA C11 C11 C 0 1 N N N -3.521 32.838 17.920 8.323 0.380 0.915 C11 ZPA 7 ZPA N8 N8 N 0 1 N N N -3.435 34.308 17.756 7.294 -0.656 0.800 N8 ZPA 8 ZPA C7 C7 C 0 1 N N N -2.603 34.826 16.735 6.133 -0.458 0.163 C7 ZPA 9 ZPA O7 O7 O 0 1 N N N -2.205 34.196 15.757 5.798 0.573 -0.381 O7 ZPA 10 ZPA C9 C9 C 0 1 N N N -3.322 35.143 18.886 7.439 -1.883 1.318 C9 ZPA 11 ZPA O9 O9 O 0 1 N N N -3.426 34.810 20.067 8.410 -2.276 1.928 O9 ZPA 12 ZPA C10 C10 C 0 1 N N N -3.022 36.560 18.381 6.200 -2.698 1.021 C10 ZPA 13 ZPA C6 C6 C 0 1 N N R -2.350 36.326 17.011 5.305 -1.722 0.230 C6 ZPA 14 ZPA S5 S5 S 0 1 N N N -0.556 36.742 17.063 3.749 -1.421 1.112 S5 ZPA 15 ZPA C4 C4 C 0 1 N N N 0.119 35.290 17.951 2.868 -0.284 0.006 C4 ZPA 16 ZPA C3 C3 C 0 1 N N N 0.054 35.342 19.489 1.511 0.073 0.617 C3 ZPA 17 ZPA C2 C2 C 0 1 N N N 0.563 33.995 20.014 0.768 1.032 -0.315 C2 ZPA 18 ZPA C1 C1 C 0 1 N N N 0.332 33.720 21.508 -0.568 1.383 0.287 C1 ZPA 19 ZPA N2 N2 N 0 1 N N N -0.715 34.224 22.123 -0.915 0.882 1.428 N2 ZPA 20 ZPA N1 N1 N 0 1 N N N 1.197 32.928 22.114 -1.415 2.234 -0.374 N1 ZPA 21 ZPA "C1'" "C1'" C 0 1 N N R 1.150 32.548 23.514 -2.713 2.576 0.212 "C1'" ZPA 22 ZPA "O5'" "O5'" O 0 1 N N N -0.216 32.266 23.850 -3.718 1.710 -0.320 "O5'" ZPA 23 ZPA "C2'" "C2'" C 0 1 N N R 1.907 33.625 24.338 -3.060 4.028 -0.129 "C2'" ZPA 24 ZPA "O2'" "O2'" O 0 1 N N N 3.292 33.270 24.453 -2.088 4.899 0.451 "O2'" ZPA 25 ZPA "C3'" "C3'" C 0 1 N N S 1.328 33.822 25.740 -4.446 4.359 0.435 "C3'" ZPA 26 ZPA "O3'" "O3'" O 0 1 N N N 1.823 35.047 26.288 -4.809 5.688 0.059 "O3'" ZPA 27 ZPA "C4'" "C4'" C 0 1 N N S -0.192 33.849 25.633 -5.466 3.368 -0.134 "C4'" ZPA 28 ZPA "O4'" "O4'" O 0 1 N N N -0.788 34.219 26.877 -6.750 3.622 0.441 "O4'" ZPA 29 ZPA "C5'" "C5'" C 0 1 N N R -0.637 32.454 25.215 -5.026 1.942 0.206 "C5'" ZPA 30 ZPA "C6'" "C6'" C 0 1 N N N -2.144 32.374 25.211 -6.009 0.944 -0.410 "C6'" ZPA 31 ZPA "O6'" "O6'" O 0 1 N N N -2.487 33.330 24.207 -5.665 -0.380 0.003 "O6'" ZPA 32 ZPA C1A C1A C 0 1 N N S -3.891 33.484 24.062 -6.525 -1.394 -0.521 C1A ZPA 33 ZPA O5A O5A O 0 1 N N N -4.357 32.570 23.047 -7.842 -1.220 0.007 O5A ZPA 34 ZPA C5A C5A C 0 1 N N N -5.752 32.776 22.701 -8.793 -2.172 -0.475 C5A ZPA 35 ZPA C4A C4A C 0 1 N N R -5.998 34.217 22.232 -8.353 -3.581 -0.071 C4A ZPA 36 ZPA O4A O4A O 0 1 N N N -7.387 34.390 21.912 -9.272 -4.539 -0.600 O4A ZPA 37 ZPA C3A C3A C 0 1 N N S -5.551 35.191 23.322 -6.953 -3.850 -0.631 C3A ZPA 38 ZPA O3A O3A O 0 1 N N N -5.709 36.551 22.911 -6.504 -5.136 -0.197 O3A ZPA 39 ZPA C2A C2A C 0 1 N N R -4.078 34.929 23.605 -5.994 -2.772 -0.118 C2A ZPA 40 ZPA O2A O2A O 0 1 N N N -3.583 35.835 24.597 -4.700 -2.972 -0.693 O2A ZPA 41 ZPA H1 H1 H 0 1 N N N -1.236 31.694 16.948 8.117 1.636 -1.467 H1 ZPA 42 ZPA H2 H2 H 0 1 N N N 0.513 30.467 18.181 9.646 1.486 -3.392 H2 ZPA 43 ZPA H3 H3 H 0 1 N N N 0.314 30.135 20.621 11.650 0.061 -3.264 H3 ZPA 44 ZPA H4 H4 H 0 1 N N N -1.652 31.032 21.829 12.123 -1.217 -1.213 H4 ZPA 45 ZPA H5 H5 H 0 1 N N N -3.383 32.285 20.595 10.593 -1.069 0.710 H5 ZPA 46 ZPA H6 H6 H 0 1 N N N -4.469 32.629 18.438 8.884 0.234 1.838 H6 ZPA 47 ZPA H7 H7 H 0 1 N N N -3.552 32.405 16.909 7.849 1.362 0.929 H7 ZPA 48 ZPA H8 H8 H 0 1 N N N -2.341 37.085 19.067 6.449 -3.567 0.411 H8 ZPA 49 ZPA H9 H9 H 0 1 N N N -3.949 37.141 18.269 5.714 -3.008 1.946 H9 ZPA 50 ZPA H10 H10 H 0 1 N N N -2.812 36.952 16.234 5.110 -2.106 -0.771 H10 ZPA 51 ZPA H11 H11 H 0 1 N N N -0.443 34.404 17.621 3.457 0.623 -0.126 H11 ZPA 52 ZPA H12 H12 H 0 1 N N N 1.175 35.182 17.663 2.715 -0.763 -0.961 H12 ZPA 53 ZPA H13 H13 H 0 1 N N N 0.690 36.157 19.865 0.922 -0.835 0.750 H13 ZPA 54 ZPA H14 H14 H 0 1 N N N -0.983 35.506 19.816 1.663 0.552 1.585 H14 ZPA 55 ZPA H15 H15 H 0 1 N N N 0.059 33.200 19.444 1.357 1.939 -0.447 H15 ZPA 56 ZPA H16 H16 H 0 1 N N N 1.646 33.949 19.828 0.616 0.553 -1.282 H16 ZPA 57 ZPA H17 H17 H 0 1 N N N -0.763 33.934 23.079 -1.775 1.109 1.815 H17 ZPA 58 ZPA H18 H18 H 0 1 N N N 1.946 32.560 21.563 -1.154 2.610 -1.229 H18 ZPA 59 ZPA H19 H19 H 0 1 N N N 1.722 31.615 23.624 -2.667 2.457 1.294 H19 ZPA 60 ZPA H20 H20 H 0 1 N N N 1.822 34.580 23.798 -3.066 4.157 -1.211 H20 ZPA 61 ZPA H21 H21 H 0 1 N N N 3.748 33.933 24.958 -1.185 4.742 0.142 H21 ZPA 62 ZPA H22 H22 H 0 1 N N N 1.627 32.973 26.372 -4.425 4.279 1.522 H22 ZPA 63 ZPA H23 H23 H 0 1 N N N 1.465 35.172 27.159 -4.201 6.368 0.381 H23 ZPA 64 ZPA H24 H24 H 0 1 N N N -0.480 34.564 24.848 -5.523 3.485 -1.216 H24 ZPA 65 ZPA H25 H25 H 0 1 N N N -0.499 35.091 27.120 -7.089 4.511 0.269 H25 ZPA 66 ZPA H26 H26 H 0 1 N N N -0.207 31.694 25.884 -5.010 1.815 1.289 H26 ZPA 67 ZPA H27 H27 H 0 1 N N N -2.562 32.654 26.189 -7.020 1.177 -0.077 H27 ZPA 68 ZPA H28 H28 H 0 1 N N N -2.490 31.366 24.939 -5.960 1.010 -1.497 H28 ZPA 69 ZPA H29 H29 H 0 1 N N N -4.416 33.321 25.015 -6.556 -1.319 -1.607 H29 ZPA 70 ZPA H30 H30 H 0 1 N N N -6.375 32.575 23.585 -9.771 -1.958 -0.043 H30 ZPA 71 ZPA H31 H31 H 0 1 N N N -6.028 32.083 21.892 -8.854 -2.107 -1.561 H31 ZPA 72 ZPA H32 H32 H 0 1 N N N -5.387 34.397 21.335 -8.331 -3.658 1.016 H32 ZPA 73 ZPA H33 H33 H 0 1 N N N -7.537 35.282 21.622 -10.181 -4.425 -0.291 H33 ZPA 74 ZPA H34 H34 H 0 1 N N N -6.132 34.997 24.235 -6.985 -3.822 -1.720 H34 ZPA 75 ZPA H35 H35 H 0 1 N N N -5.423 37.128 23.609 -7.070 -5.867 -0.481 H35 ZPA 76 ZPA H36 H36 H 0 1 N N N -3.517 35.069 22.669 -5.924 -2.833 0.968 H36 ZPA 77 ZPA H37 H37 H 0 1 N N N -2.664 35.656 24.760 -4.041 -2.323 -0.411 H37 ZPA 78 # # 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 ZPA O7 C7 DOUB N N 1 ZPA C7 C6 SING N N 2 ZPA C7 N8 SING N N 3 ZPA C6 S5 SING N N 4 ZPA C6 C10 SING N N 5 ZPA S5 C4 SING N N 6 ZPA N8 C11 SING N N 7 ZPA N8 C9 SING N N 8 ZPA C11 C12 SING N N 9 ZPA C4 C3 SING N N 10 ZPA C13 C12 DOUB Y N 11 ZPA C13 C14 SING Y N 12 ZPA C10 C9 SING N N 13 ZPA C12 C17 SING Y N 14 ZPA C14 C15 DOUB Y N 15 ZPA C9 O9 DOUB N N 16 ZPA C3 C2 SING N N 17 ZPA C2 C1 SING N N 18 ZPA C17 C16 DOUB Y N 19 ZPA C15 C16 SING Y N 20 ZPA C1 N1 SING N N 21 ZPA C1 N2 DOUB N N 22 ZPA O4A C4A SING N N 23 ZPA N1 "C1'" SING N N 24 ZPA C4A C5A SING N N 25 ZPA C4A C3A SING N N 26 ZPA C5A O5A SING N N 27 ZPA O3A C3A SING N N 28 ZPA O5A C1A SING N N 29 ZPA C3A C2A SING N N 30 ZPA "C1'" "O5'" SING N N 31 ZPA "C1'" "C2'" SING N N 32 ZPA C2A C1A SING N N 33 ZPA C2A O2A SING N N 34 ZPA "O5'" "C5'" SING N N 35 ZPA C1A "O6'" SING N N 36 ZPA "O6'" "C6'" SING N N 37 ZPA "C2'" "O2'" SING N N 38 ZPA "C2'" "C3'" SING N N 39 ZPA "C6'" "C5'" SING N N 40 ZPA "C5'" "C4'" SING N N 41 ZPA "C4'" "C3'" SING N N 42 ZPA "C4'" "O4'" SING N N 43 ZPA "C3'" "O3'" SING N N 44 ZPA C13 H1 SING N N 45 ZPA C14 H2 SING N N 46 ZPA C15 H3 SING N N 47 ZPA C16 H4 SING N N 48 ZPA C17 H5 SING N N 49 ZPA C11 H6 SING N N 50 ZPA C11 H7 SING N N 51 ZPA C10 H8 SING N N 52 ZPA C10 H9 SING N N 53 ZPA C6 H10 SING N N 54 ZPA C4 H11 SING N N 55 ZPA C4 H12 SING N N 56 ZPA C3 H13 SING N N 57 ZPA C3 H14 SING N N 58 ZPA C2 H15 SING N N 59 ZPA C2 H16 SING N N 60 ZPA N2 H17 SING N N 61 ZPA N1 H18 SING N N 62 ZPA "C1'" H19 SING N N 63 ZPA "C2'" H20 SING N N 64 ZPA "O2'" H21 SING N N 65 ZPA "C3'" H22 SING N N 66 ZPA "O3'" H23 SING N N 67 ZPA "C4'" H24 SING N N 68 ZPA "O4'" H25 SING N N 69 ZPA "C5'" H26 SING N N 70 ZPA "C6'" H27 SING N N 71 ZPA "C6'" H28 SING N N 72 ZPA C1A H29 SING N N 73 ZPA C5A H30 SING N N 74 ZPA C5A H31 SING N N 75 ZPA C4A H32 SING N N 76 ZPA O4A H33 SING N N 77 ZPA C3A H34 SING N N 78 ZPA O3A H35 SING N N 79 ZPA C2A H36 SING N N 80 ZPA O2A H37 SING N N 81 # # 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 ZPA SMILES ACDLabs 12.01 "O=C3N(C(=O)CC3SCCCC(=[N@H])NC2OC(COC1OCC(O)C(O)C1O)C(O)C(O)C2O)Cc4ccccc4" ZPA InChI InChI 1.03 "InChI=1S/C26H37N3O11S/c27-17(7-4-8-41-16-9-18(31)29(25(16)37)10-13-5-2-1-3-6-13)28-24-22(35)21(34)20(33)15(40-24)12-39-26-23(36)19(32)14(30)11-38-26/h1-3,5-6,14-16,19-24,26,30,32-36H,4,7-12H2,(H2,27,28)/t14-,15-,16-,19+,20-,21+,22-,23-,24-,26+/m1/s1" ZPA InChIKey InChI 1.03 MKGCRBLJKRCKKQ-OGJWHHEUSA-N ZPA SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)CCCS[C@@H]3CC(=O)N(Cc4ccccc4)C3=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O" ZPA SMILES CACTVS 3.385 "O[CH]1CO[CH](OC[CH]2O[CH](NC(=N)CCCS[CH]3CC(=O)N(Cc4ccccc4)C3=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O" ZPA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C(/CCCS[C@@H]1CC(=O)N(C1=O)Cc2ccccc2)\N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO[C@H]4[C@@H]([C@H]([C@@H](CO4)O)O)O)O)O)O" ZPA SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CN2C(=O)CC(C2=O)SCCCC(=N)NC3C(C(C(C(O3)COC4C(C(C(CO4)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 ZPA "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(1Z)-4-{[(3R)-1-benzyl-2,5-dioxopyrrolidin-3-yl]sulfanyl}butanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine" ZPA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-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]butanimidamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZPA "Create component" 2014-01-31 PDBJ ZPA "Modify name" 2014-02-18 PDBJ ZPA "Modify synonyms" 2014-02-18 PDBJ ZPA "Initial release" 2014-04-23 RCSB ZPA "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id ZPA _pdbx_chem_comp_synonyms.name "4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-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]butanimidamide" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##