data_RY7 # _chem_comp.id RY7 _chem_comp.name "4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H25 N O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-03-02 _chem_comp.pdbx_modified_date 2020-07-17 _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 323.340 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RY7 _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 1GAI _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 RY7 C1A C1A C 0 1 N N S 33.170 20.622 8.181 0.855 -0.516 1.181 C1A RY7 1 RY7 C2A C2A C 0 1 N N S 34.370 20.482 9.121 1.391 0.892 1.445 C2A RY7 2 RY7 C3A C3A C 0 1 N N S 33.998 19.616 10.323 2.185 1.371 0.228 C3A RY7 3 RY7 C4A C4A C 0 1 N N R 32.901 20.289 11.143 3.355 0.419 -0.025 C4A RY7 4 RY7 C5A C5A C 0 1 N N R 31.630 20.514 10.300 2.819 -0.989 -0.289 C5A RY7 5 RY7 C6A C6A C 0 1 N N N 30.612 21.349 11.082 3.989 -1.942 -0.541 C6A RY7 6 RY7 C7A C7A C 0 1 N N N 31.948 21.184 8.934 2.025 -1.469 0.928 C7A RY7 7 RY7 O2A O2A O 0 1 N N N 35.453 19.879 8.431 0.298 1.781 1.681 O2A RY7 8 RY7 O3A O3A O 0 1 N N N 35.144 19.427 11.142 2.685 2.687 0.474 O3A RY7 9 RY7 O4A O4A O 0 1 N N N 32.594 19.474 12.273 4.096 0.867 -1.162 O4A RY7 10 RY7 O6A O6A O 0 1 N N N 31.127 22.642 11.401 4.661 -1.562 -1.744 O6A RY7 11 RY7 C1 C1 C 0 1 N N S 31.706 18.270 3.522 -4.229 -0.463 -0.224 C1 RY7 12 RY7 C2 C2 C 0 1 N N R 33.179 18.615 3.786 -3.539 0.903 -0.241 C2 RY7 13 RY7 C3 C3 C 0 1 N N S 33.494 18.445 5.286 -2.064 0.716 -0.609 C3 RY7 14 RY7 C4 C4 C 0 1 N N S 32.573 19.381 6.087 -1.418 -0.249 0.389 C4 RY7 15 RY7 C5 C5 C 0 1 N N R 31.127 18.938 5.790 -2.190 -1.571 0.382 C5 RY7 16 RY7 C6 C6 C 0 1 N N N 30.066 19.772 6.483 -1.588 -2.519 1.421 C6 RY7 17 RY7 N4 N4 N 0 1 N N N 32.876 19.318 7.536 -0.022 -0.494 0.003 N4 RY7 18 RY7 O2 O2 O 0 1 N N N 34.002 17.737 3.025 -4.169 1.745 -1.209 O2 RY7 19 RY7 O3 O3 O 0 1 N N N 34.864 18.740 5.542 -1.394 1.977 -0.557 O3 RY7 20 RY7 O5 O5 O 0 1 N N N 30.863 19.049 4.371 -3.561 -1.322 0.702 O5 RY7 21 RY7 O1 O1 O 0 1 N Y N 31.575 16.907 3.824 -4.178 -1.040 -1.530 O1 RY7 22 RY7 H1A H1A H 0 1 N N N 33.440 21.344 7.396 0.289 -0.858 2.048 H1A RY7 23 RY7 H2A H2A H 0 1 N N N 34.656 21.482 9.480 2.041 0.876 2.319 H2A RY7 24 RY7 H3A H3A H 0 1 N N N 33.625 18.647 9.960 1.534 1.388 -0.647 H3A RY7 25 RY7 H4A H4A H 0 1 N N N 33.269 21.269 11.480 4.006 0.403 0.849 H4A RY7 26 RY7 H5A H5A H 0 1 N N N 31.180 19.531 10.096 2.168 -0.973 -1.163 H5A RY7 27 RY7 H6A1 H6A1 H 0 0 N N N 29.704 21.467 10.473 4.686 -1.891 0.295 H6A1 RY7 28 RY7 H6A2 H6A2 H 0 0 N N N 30.362 20.824 12.016 3.614 -2.960 -0.641 H6A2 RY7 29 RY7 H7A1 H7A1 H 0 0 N N N 32.126 22.254 9.116 2.676 -1.485 1.803 H7A1 RY7 30 RY7 H7A2 H7A2 H 0 0 N N N 31.067 21.064 8.286 1.643 -2.472 0.741 H7A2 RY7 31 RY7 HOA2 HOA2 H 0 0 N N N 36.195 19.794 9.018 0.564 2.694 1.855 HOA2 RY7 32 RY7 HOA3 HOA3 H 0 0 N N N 34.914 18.888 11.890 3.200 3.055 -0.258 HOA3 RY7 33 RY7 HOA4 HOA4 H 0 0 N N N 33.380 19.338 12.789 4.467 1.755 -1.065 HOA4 RY7 34 RY7 HOA6 HOA6 H 0 0 N N N 30.473 23.133 11.884 5.416 -2.124 -1.967 HOA6 RY7 35 RY7 H1 H1 H 0 1 N N N 31.475 18.463 2.464 -5.269 -0.341 0.079 H1 RY7 36 RY7 H2 H2 H 0 1 N N N 33.360 19.661 3.499 -3.613 1.361 0.745 H2 RY7 37 RY7 H3 H3 H 0 1 N N N 33.272 17.407 5.573 -1.988 0.305 -1.616 H3 RY7 38 RY7 H4 H4 H 0 1 N N N 32.710 20.411 5.725 -1.448 0.186 1.388 H4 RY7 39 RY7 H5 H5 H 0 1 N N N 31.014 17.890 6.106 -2.124 -2.025 -0.606 H5 RY7 40 RY7 H62 H62 H 0 1 N N N 30.216 19.726 7.572 -1.551 -2.021 2.390 H62 RY7 41 RY7 H63 H63 H 0 1 N N N 30.143 20.816 6.146 -2.205 -3.415 1.496 H63 RY7 42 RY7 H61 H61 H 0 1 N N N 29.070 19.379 6.233 -0.579 -2.797 1.117 H61 RY7 43 RY7 HN41 HN41 H 0 0 N N N 32.086 18.915 7.999 0.062 -1.349 -0.526 HN41 RY7 44 RY7 HO2 HO2 H 0 1 N Y N 34.916 17.943 3.182 -5.109 1.902 -1.040 HO2 RY7 45 RY7 HO3 HO3 H 0 1 N Y N 35.044 18.631 6.468 -1.756 2.641 -1.160 HO3 RY7 46 RY7 HO1 HO1 H 0 1 N Y N 30.677 16.635 3.678 -4.598 -1.909 -1.594 HO1 RY7 47 # # 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 RY7 O2 C2 SING N N 1 RY7 C1 C2 SING N N 2 RY7 C1 O1 SING N N 3 RY7 C1 O5 SING N N 4 RY7 C2 C3 SING N N 5 RY7 O5 C5 SING N N 6 RY7 C3 O3 SING N N 7 RY7 C3 C4 SING N N 8 RY7 C5 C4 SING N N 9 RY7 C5 C6 SING N N 10 RY7 C4 N4 SING N N 11 RY7 N4 C1A SING N N 12 RY7 C1A C7A SING N N 13 RY7 C1A C2A SING N N 14 RY7 O2A C2A SING N N 15 RY7 C7A C5A SING N N 16 RY7 C2A C3A SING N N 17 RY7 C5A C6A SING N N 18 RY7 C5A C4A SING N N 19 RY7 C3A O3A SING N N 20 RY7 C3A C4A SING N N 21 RY7 C6A O6A SING N N 22 RY7 C4A O4A SING N N 23 RY7 C1A H1A SING N N 24 RY7 C2A H2A SING N N 25 RY7 C3A H3A SING N N 26 RY7 C4A H4A SING N N 27 RY7 C5A H5A SING N N 28 RY7 C6A H6A1 SING N N 29 RY7 C6A H6A2 SING N N 30 RY7 C7A H7A1 SING N N 31 RY7 C7A H7A2 SING N N 32 RY7 O2A HOA2 SING N N 33 RY7 O3A HOA3 SING N N 34 RY7 O4A HOA4 SING N N 35 RY7 O6A HOA6 SING N N 36 RY7 C1 H1 SING N N 37 RY7 C2 H2 SING N N 38 RY7 C3 H3 SING N N 39 RY7 C4 H4 SING N N 40 RY7 C5 H5 SING N N 41 RY7 C6 H62 SING N N 42 RY7 C6 H63 SING N N 43 RY7 C6 H61 SING N N 44 RY7 N4 HN41 SING N N 45 RY7 O2 HO2 SING N N 46 RY7 O3 HO3 SING N N 47 RY7 O1 HO1 SING N N 48 # # 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 RY7 SMILES ACDLabs 12.01 "C1(CC(C(C(C1O)O)O)CO)NC2C(C(C(O)OC2C)O)O" RY7 InChI InChI 1.03 "InChI=1S/C13H25NO8/c1-4-7(10(18)12(20)13(21)22-4)14-6-2-5(3-15)8(16)11(19)9(6)17/h4-21H,2-3H2,1H3/t4-,5-,6+,7-,8-,9+,10+,11+,12-,13+/m1/s1" RY7 InChIKey InChI 1.03 PFUNPXBPUXETIR-KJEWDVBSSA-N RY7 SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1N[C@H]2C[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O" RY7 SMILES CACTVS 3.385 "C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N[CH]2C[CH](CO)[CH](O)[CH](O)[CH]2O" RY7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)N[C@H]2C[C@@H]([C@H]([C@@H]([C@H]2O)O)O)CO" RY7 SMILES "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(C(O1)O)O)O)NC2CC(C(C(C2O)O)O)CO" # # 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 RY7 "SYSTEMATIC NAME" ACDLabs 12.01 "4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose" RY7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{R},4~{S},5~{S},6~{R})-5-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]amino]-6-methyl-oxane-2,3,4-triol" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support RY7 "CARBOHYDRATE ISOMER" D PDB ? RY7 "CARBOHYDRATE RING" pyranose PDB ? RY7 "CARBOHYDRATE ANOMER" alpha PDB ? RY7 "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RY7 "Create component" 2020-03-02 RCSB RY7 "Modify name" 2020-06-01 RCSB RY7 "Initial release" 2020-07-29 RCSB ##