data_YKR # _chem_comp.id YKR _chem_comp.name 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H19 N O5" _chem_comp.mon_nstd_parent_comp_id PA1 _chem_comp.pdbx_synonyms ;4-benzyl-alpha-D-glucosamine; 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucose; 2-amino-4-O-benzyl-2-deoxy-D-glucose; 2-amino-4-O-benzyl-2-deoxy-glucose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-07-31 _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 269.294 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YKR _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 4B3S _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 YKR 4-benzyl-alpha-D-glucosamine PDB ? 2 YKR 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucose PDB ? 3 YKR 2-amino-4-O-benzyl-2-deoxy-D-glucose PDB ? 4 YKR 2-amino-4-O-benzyl-2-deoxy-glucose PDB ? # # 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 YKR C1 C1 C 0 1 N N S 190.255 87.059 -11.126 -3.615 -0.031 -0.120 C1 YKR 1 YKR O1 O1 O 0 1 N Y N 190.932 88.324 -11.034 -3.604 0.024 -1.547 O1 YKR 2 YKR C2 C2 C 0 1 N N R 188.865 87.213 -10.475 -2.953 1.228 0.445 C2 YKR 3 YKR N2 N2 N 0 1 N N N 188.082 88.225 -11.188 -3.656 2.418 -0.051 N2 YKR 4 YKR C3 C3 C 0 1 N N R 189.037 87.614 -9.001 -1.490 1.273 -0.006 C3 YKR 5 YKR O3 O3 O 0 1 N N N 187.753 87.768 -8.372 -0.844 2.406 0.576 O3 YKR 6 YKR C4 C4 C 0 1 N N S 189.875 86.543 -8.274 -0.787 -0.009 0.451 C4 YKR 7 YKR O4 O4 O 0 1 N N N 190.075 86.925 -6.894 0.560 -0.012 -0.028 O4 YKR 8 YKR C5 C5 C 0 1 N N R 191.258 86.409 -9.007 -1.533 -1.221 -0.115 C5 YKR 9 YKR O5 O5 O 0 1 N N N 191.041 86.054 -10.423 -2.894 -1.184 0.318 O5 YKR 10 YKR C6 C6 C 0 1 N N N 192.133 85.326 -8.322 -0.872 -2.506 0.387 C6 YKR 11 YKR O6 O6 O 0 1 N N N 192.709 84.442 -9.290 -1.498 -3.635 -0.227 O6 YKR 12 YKR CAL CAL C 0 1 Y N N 189.193 86.691 -2.354 4.745 1.179 -0.906 CAL YKR 13 YKR CAM CAM C 0 1 Y N N 188.958 86.378 -3.725 3.470 1.329 -0.395 CAM YKR 14 YKR CAN CAN C 0 1 Y N N 190.536 86.777 -1.865 5.454 0.017 -0.665 CAN YKR 15 YKR CAO CAO C 0 1 Y N N 190.059 86.147 -4.604 2.903 0.318 0.358 CAO YKR 16 YKR CAP CAP C 0 1 Y N N 191.639 86.546 -2.746 4.887 -0.995 0.087 CAP YKR 17 YKR CAU CAU C 0 1 N N N 189.847 85.852 -5.947 1.513 0.482 0.916 CAU YKR 18 YKR CBC CBC C 0 1 Y N N 191.399 86.233 -4.112 3.612 -0.844 0.599 CBC YKR 19 YKR H1 H1 H 0 1 N N N 190.126 86.769 -12.179 -4.645 -0.090 0.234 H1 YKR 20 YKR H2 H2 H 0 1 N N N 188.346 86.244 -10.519 -2.998 1.206 1.534 H2 YKR 21 YKR HN21 HN2 H 0 0 N N N 187.184 88.316 -10.758 -4.625 2.409 0.230 HN21 YKR 22 YKR HN22 HN2A H 0 0 N Y N 188.560 89.103 -11.151 -3.199 3.263 0.256 HN22 YKR 23 YKR H3 H3 H 0 1 N N N 189.585 88.567 -8.963 -1.446 1.347 -1.093 H3 YKR 24 YKR HO3 HO3 H 0 1 N Y N 187.873 88.016 -7.463 -1.242 3.253 0.335 HO3 YKR 25 YKR H4 H4 H 0 1 N N N 189.351 85.578 -8.332 -0.786 -0.056 1.540 H4 YKR 26 YKR H5 H5 H 0 1 N N N 191.780 87.375 -8.944 -1.497 -1.194 -1.204 H5 YKR 27 YKR H61 H6 H 0 1 N N N 192.940 85.819 -7.760 0.187 -2.494 0.130 H61 YKR 28 YKR H62 H6A H 0 1 N N N 191.507 84.743 -7.630 -0.982 -2.573 1.469 H62 YKR 29 YKR HO6 HO6 H 0 1 N Y N 193.239 83.789 -8.848 -1.129 -4.486 0.045 HO6 YKR 30 YKR HAL HAL H 0 1 N N N 188.361 86.863 -1.687 5.186 1.968 -1.498 HAL YKR 31 YKR HAM HAM H 0 1 N N N 187.947 86.316 -4.099 2.916 2.237 -0.583 HAM YKR 32 YKR HAN HAN H 0 1 N N N 190.717 87.017 -0.828 6.450 -0.101 -1.065 HAN YKR 33 YKR HAP HAP H 0 1 N N N 192.651 86.609 -2.375 5.440 -1.903 0.274 HAP YKR 34 YKR HAU HAU H 0 1 N N N 188.801 85.528 -6.056 1.321 1.537 1.108 HAU YKR 35 YKR HAUA HAUA H 0 0 N N N 190.518 85.022 -6.216 1.426 -0.079 1.847 HAUA YKR 36 YKR HBC HBC H 0 1 N N N 192.230 86.060 -4.779 3.169 -1.635 1.187 HBC YKR 37 YKR HO1 H7 H 0 1 N Y N 191.793 88.253 -11.430 -4.009 -0.743 -1.974 HO1 YKR 38 # # 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 YKR C1 O1 SING N N 1 YKR C1 C2 SING N N 2 YKR C1 O5 SING N N 3 YKR C2 N2 SING N N 4 YKR C2 C3 SING N N 5 YKR C3 O3 SING N N 6 YKR C3 C4 SING N N 7 YKR C4 O4 SING N N 8 YKR C4 C5 SING N N 9 YKR O4 CAU SING N N 10 YKR C5 O5 SING N N 11 YKR C5 C6 SING N N 12 YKR C6 O6 SING N N 13 YKR CAL CAM DOUB Y N 14 YKR CAL CAN SING Y N 15 YKR CAM CAO SING Y N 16 YKR CAN CAP DOUB Y N 17 YKR CAO CAU SING N N 18 YKR CAO CBC DOUB Y N 19 YKR CAP CBC SING Y N 20 YKR C1 H1 SING N N 21 YKR C2 H2 SING N N 22 YKR N2 HN21 SING N N 23 YKR N2 HN22 SING N N 24 YKR C3 H3 SING N N 25 YKR O3 HO3 SING N N 26 YKR C4 H4 SING N N 27 YKR C5 H5 SING N N 28 YKR C6 H61 SING N N 29 YKR C6 H62 SING N N 30 YKR O6 HO6 SING N N 31 YKR CAL HAL SING N N 32 YKR CAM HAM SING N N 33 YKR CAN HAN SING N N 34 YKR CAP HAP SING N N 35 YKR CAU HAU SING N N 36 YKR CAU HAUA SING N N 37 YKR CBC HBC SING N N 38 YKR O1 HO1 SING N N 39 # # 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 YKR SMILES ACDLabs 12.01 "OC2C(OCc1ccccc1)C(OC(O)C2N)CO" YKR InChI InChI 1.03 "InChI=1S/C13H19NO5/c14-10-11(16)12(9(6-15)19-13(10)17)18-7-8-4-2-1-3-5-8/h1-5,9-13,15-17H,6-7,14H2/t9-,10-,11-,12-,13+/m1/s1" YKR InChIKey InChI 1.03 IFOCVXNXLGGVEE-VEGXAWMVSA-N YKR SMILES_CANONICAL CACTVS 3.385 "N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](OCc2ccccc2)[C@@H]1O" YKR SMILES CACTVS 3.385 "N[CH]1[CH](O)O[CH](CO)[CH](OCc2ccccc2)[CH]1O" YKR SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1ccc(cc1)CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)N)O)CO" YKR SMILES "OpenEye OEToolkits" 1.9.2 "c1ccc(cc1)COC2C(OC(C(C2O)N)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 YKR "SYSTEMATIC NAME" ACDLabs 12.01 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose YKR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S,3R,4R,5S,6R)-3-azanyl-6-(hydroxymethyl)-5-phenylmethoxy-oxane-2,4-diol" # _pdbx_chem_comp_related.comp_id YKR _pdbx_chem_comp_related.related_comp_id PA1 _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 YKR C1 PA1 C1 "Carbohydrate core" 2 YKR C2 PA1 C2 "Carbohydrate core" 3 YKR C3 PA1 C3 "Carbohydrate core" 4 YKR C4 PA1 C4 "Carbohydrate core" 5 YKR C5 PA1 C5 "Carbohydrate core" 6 YKR C6 PA1 C6 "Carbohydrate core" 7 YKR N2 PA1 N2 "Carbohydrate core" 8 YKR O1 PA1 O1 "Carbohydrate core" 9 YKR O3 PA1 O3 "Carbohydrate core" 10 YKR O4 PA1 O4 "Carbohydrate core" 11 YKR O5 PA1 O5 "Carbohydrate core" 12 YKR O6 PA1 O6 "Carbohydrate core" 13 YKR H1 PA1 H1 "Carbohydrate core" 14 YKR H2 PA1 H2 "Carbohydrate core" 15 YKR H3 PA1 H3 "Carbohydrate core" 16 YKR H4 PA1 H4 "Carbohydrate core" 17 YKR H5 PA1 H5 "Carbohydrate core" 18 YKR H61 PA1 H61 "Carbohydrate core" 19 YKR H62 PA1 H62 "Carbohydrate core" 20 YKR HO1 PA1 HO1 "Carbohydrate core" 21 YKR HN21 PA1 HN21 "Carbohydrate core" 22 YKR HN22 PA1 HN22 "Carbohydrate core" 23 YKR HO3 PA1 HO3 "Carbohydrate core" 24 YKR HO6 PA1 HO6 "Carbohydrate core" # # 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 YKR "CARBOHYDRATE ISOMER" D PDB ? YKR "CARBOHYDRATE RING" pyranose PDB ? YKR "CARBOHYDRATE ANOMER" alpha PDB ? YKR "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 YKR "Create component" 2012-07-31 EBI YKR "Initial release" 2013-08-07 RCSB YKR "Modify descriptor" 2014-09-05 RCSB YKR "Other modification" 2020-07-03 RCSB YKR "Modify parent residue" 2020-07-17 RCSB YKR "Modify synonyms" 2020-07-17 RCSB YKR "Modify internal type" 2020-07-17 RCSB YKR "Modify linking type" 2020-07-17 RCSB YKR "Modify atom id" 2020-07-17 RCSB YKR "Modify component atom id" 2020-07-17 RCSB YKR "Modify leaving atom flag" 2020-07-17 RCSB ##