data_NM9 # _chem_comp.id NM9 _chem_comp.name "methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranoside" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C12 H22 N2 O7" _chem_comp.mon_nstd_parent_comp_id NAG _chem_comp.pdbx_synonyms ;(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]oxypropanamide; methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucoside; methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-D-glucoside; methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-glucoside ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-19 _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 306.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NM9 _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 4CFO _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 NM9 "(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]oxypropanamide" PDB ? 2 NM9 "methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucoside" PDB ? 3 NM9 "methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-D-glucoside" PDB ? 4 NM9 "methyl 2-acetamido-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-glucoside" 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 NM9 C3A C3A C 0 1 N N R 1.068 33.980 -8.966 2.352 -1.214 -0.519 C3A NM9 1 NM9 C1 C1 C 0 1 N N R 3.019 33.495 -5.093 -1.601 1.082 -0.386 C1 NM9 2 NM9 N3A N3A N 0 1 N N N 2.766 33.423 -10.532 4.787 -0.784 -0.452 N3A NM9 3 NM9 O4 O4 O 0 1 N N N 1.365 30.252 -6.933 -0.940 -3.018 0.052 O4 NM9 4 NM9 O7 O2B O 0 1 N N N 0.898 36.054 -5.565 0.672 3.002 1.161 O7 NM9 5 NM9 C1B C1B C 0 1 N N N 4.983 34.562 -4.771 -3.070 2.964 -0.592 C1B NM9 6 NM9 C3B C3B C 0 1 N N N -0.408 33.865 -8.997 2.446 -2.574 -1.212 C3B NM9 7 NM9 C2 C2 C 0 1 N N R 2.881 33.756 -6.521 -0.233 0.668 0.161 C2 NM9 8 NM9 C3E C3E C 0 1 N N N 1.971 34.397 -10.083 3.633 -0.939 0.226 C3E NM9 9 NM9 C3 C3 C 0 1 N N R 1.852 32.750 -7.008 0.015 -0.807 -0.169 C3 NM9 10 NM9 C4 C4 C 0 1 N N S 2.330 31.276 -6.739 -1.123 -1.648 0.416 C4 NM9 11 NM9 C5 C5 C 0 1 N N R 2.792 31.189 -5.297 -2.457 -1.145 -0.141 C5 NM9 12 NM9 C6 C5A C 0 1 N N N 3.769 30.138 -4.898 -3.604 -1.941 0.485 C6 NM9 13 NM9 C7 C2A C 0 1 N N N 1.826 36.142 -6.269 1.192 2.644 0.125 C7 NM9 14 NM9 C8 C2B C 0 1 N N N 2.195 37.459 -6.775 2.266 3.490 -0.510 C8 NM9 15 NM9 N2 N2A N 0 1 N N N 2.692 35.130 -6.693 0.811 1.490 -0.457 N2 NM9 16 NM9 OCA OCA O 0 1 N N N 2.059 35.500 -10.527 3.625 -0.858 1.436 OCA NM9 17 NM9 O1 O1A O 0 1 N N N 3.802 34.248 -4.244 -1.864 2.441 -0.033 O1 NM9 18 NM9 O3 O3A O 0 1 N N N 1.587 32.994 -8.344 1.258 -1.222 0.401 O3 NM9 19 NM9 O6 O5A O 0 1 N N N 3.284 30.012 -3.636 -4.839 -1.552 -0.119 O6 NM9 20 NM9 O5 O6 O 0 1 N N N 3.580 32.263 -5.007 -2.611 0.240 0.175 O5 NM9 21 NM9 H3A H3A H 0 1 N N N 1.202 34.815 -8.263 2.192 -0.436 -1.265 H3A NM9 22 NM9 H3B1 H3B1 H 0 0 N N N -0.771 33.534 -8.013 1.492 -2.809 -1.683 H3B1 NM9 23 NM9 H3B2 H3B2 H 0 0 N N N -0.847 34.844 -9.239 3.228 -2.542 -1.971 H3B2 NM9 24 NM9 H3B3 H3B3 H 0 0 N N N -0.703 33.132 -9.762 2.686 -3.341 -0.475 H3B3 NM9 25 NM9 H1 H1 H 0 1 N N N 2.004 33.447 -4.672 -1.605 0.981 -1.471 H1 NM9 26 NM9 H2 H2 H 0 1 N N N 3.835 33.482 -6.996 -0.215 0.807 1.242 H2 NM9 27 NM9 H3A1 H3A1 H 0 0 N N N 3.440 33.617 -11.245 4.793 -0.849 -1.420 H3A1 NM9 28 NM9 H3A2 H3A2 H 0 0 N N N 2.687 32.500 -10.156 5.611 -0.607 0.027 H3A2 NM9 29 NM9 HO4 H4 H 0 1 N Y N 1.757 29.407 -6.744 -1.627 -3.610 0.390 HO4 NM9 30 NM9 H4 HA H 0 1 N N N 3.198 31.087 -7.388 -1.123 -1.557 1.502 H4 NM9 31 NM9 H1B1 H1B1 H 0 0 N N N 5.560 35.160 -4.050 -3.918 2.373 -0.246 H1B1 NM9 32 NM9 H1B2 H1B2 H 0 0 N N N 5.535 33.641 -5.008 -3.198 4.000 -0.278 H1B2 NM9 33 NM9 H1B3 H1B3 H 0 0 N N N 4.830 35.145 -5.691 -3.016 2.919 -1.680 H1B3 NM9 34 NM9 H3 H3 H 0 1 N N N 0.935 32.902 -6.420 0.047 -0.938 -1.250 H3 NM9 35 NM9 HN2 H2A H 0 1 N N N 3.388 35.503 -7.306 1.227 1.204 -1.285 HN2 NM9 36 NM9 H5 H5 H 0 1 N N N 1.913 31.145 -4.637 -2.472 -1.276 -1.223 H5 NM9 37 NM9 H61 H5A1 H 0 1 N N N 3.675 29.215 -5.490 -3.439 -3.006 0.321 H61 NM9 38 NM9 H62 H5A2 H 0 1 N N N 4.812 30.487 -4.926 -3.644 -1.740 1.556 H62 NM9 39 NM9 HO6 H5A H 0 1 N Y N 3.786 29.355 -3.168 -5.612 -2.017 0.230 HO6 NM9 40 NM9 H81 H2B1 H 0 1 N N N 1.493 38.211 -6.387 3.241 3.187 -0.128 H81 NM9 41 NM9 H82 H2B2 H 0 1 N N N 3.215 37.705 -6.446 2.241 3.355 -1.592 H82 NM9 42 NM9 H83 H2B3 H 0 1 N N N 2.156 37.454 -7.874 2.091 4.539 -0.270 H83 NM9 43 # # 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 NM9 C3A C3B SING N N 1 NM9 C3A C3E SING N N 2 NM9 C3A O3 SING N N 3 NM9 C1 C2 SING N N 4 NM9 C1 O1 SING N N 5 NM9 C1 O5 SING N N 6 NM9 N3A C3E SING N N 7 NM9 O4 C4 SING N N 8 NM9 O7 C7 DOUB N N 9 NM9 C1B O1 SING N N 10 NM9 C2 C3 SING N N 11 NM9 C2 N2 SING N N 12 NM9 C3E OCA DOUB N N 13 NM9 C3 C4 SING N N 14 NM9 C3 O3 SING N N 15 NM9 C4 C5 SING N N 16 NM9 C5 C6 SING N N 17 NM9 C5 O5 SING N N 18 NM9 C6 O6 SING N N 19 NM9 C7 C8 SING N N 20 NM9 C7 N2 SING N N 21 NM9 C3A H3A SING N N 22 NM9 C3B H3B1 SING N N 23 NM9 C3B H3B2 SING N N 24 NM9 C3B H3B3 SING N N 25 NM9 C1 H1 SING N N 26 NM9 C2 H2 SING N N 27 NM9 N3A H3A1 SING N N 28 NM9 N3A H3A2 SING N N 29 NM9 O4 HO4 SING N N 30 NM9 C4 H4 SING N N 31 NM9 C1B H1B1 SING N N 32 NM9 C1B H1B2 SING N N 33 NM9 C1B H1B3 SING N N 34 NM9 C3 H3 SING N N 35 NM9 N2 HN2 SING N N 36 NM9 C5 H5 SING N N 37 NM9 C6 H61 SING N N 38 NM9 C6 H62 SING N N 39 NM9 O6 HO6 SING N N 40 NM9 C8 H81 SING N N 41 NM9 C8 H82 SING N N 42 NM9 C8 H83 SING N N 43 # # 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 NM9 SMILES ACDLabs 12.01 "O=C(N)C(OC1C(O)C(OC(OC)C1NC(=O)C)CO)C" NM9 InChI InChI 1.03 "InChI=1S/C12H22N2O7/c1-5(11(13)18)20-10-8(14-6(2)16)12(19-3)21-7(4-15)9(10)17/h5,7-10,12,15,17H,4H2,1-3H3,(H2,13,18)(H,14,16)/t5-,7-,8-,9-,10-,12-/m1/s1" NM9 InChIKey InChI 1.03 RDTUJRBFQHDOEJ-PKKPQKKZSA-N NM9 SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H](C)C(N)=O)[C@H]1NC(C)=O" NM9 SMILES CACTVS 3.385 "CO[CH]1O[CH](CO)[CH](O)[CH](O[CH](C)C(N)=O)[CH]1NC(C)=O" NM9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H](C(=O)N)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1O)CO)OC)NC(=O)C" NM9 SMILES "OpenEye OEToolkits" 1.7.6 "CC(C(=O)N)OC1C(C(OC(C1O)CO)OC)NC(=O)C" # # 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 NM9 "SYSTEMATIC NAME" ACDLabs 12.01 "methyl 2-(acetylamino)-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranoside" NM9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]oxypropanamide" # _pdbx_chem_comp_related.comp_id NM9 _pdbx_chem_comp_related.related_comp_id NAG _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 NM9 C1 NAG C1 "Carbohydrate core" 2 NM9 C2 NAG C2 "Carbohydrate core" 3 NM9 C7 NAG C7 "Carbohydrate core" 4 NM9 C8 NAG C8 "Carbohydrate core" 5 NM9 C3 NAG C3 "Carbohydrate core" 6 NM9 C4 NAG C4 "Carbohydrate core" 7 NM9 C5 NAG C5 "Carbohydrate core" 8 NM9 C6 NAG C6 "Carbohydrate core" 9 NM9 N2 NAG N2 "Carbohydrate core" 10 NM9 O1 NAG O1 "Carbohydrate core" 11 NM9 O7 NAG O7 "Carbohydrate core" 12 NM9 O3 NAG O3 "Carbohydrate core" 13 NM9 O4 NAG O4 "Carbohydrate core" 14 NM9 O6 NAG O6 "Carbohydrate core" 15 NM9 O5 NAG O5 "Carbohydrate core" 16 NM9 H1 NAG H1 "Carbohydrate core" 17 NM9 H2 NAG H2 "Carbohydrate core" 18 NM9 HN2 NAG HN2 "Carbohydrate core" 19 NM9 H81 NAG H81 "Carbohydrate core" 20 NM9 H82 NAG H82 "Carbohydrate core" 21 NM9 H83 NAG H83 "Carbohydrate core" 22 NM9 H3 NAG H3 "Carbohydrate core" 23 NM9 HO4 NAG HO4 "Carbohydrate core" 24 NM9 H5 NAG H5 "Carbohydrate core" 25 NM9 HO6 NAG HO6 "Carbohydrate core" 26 NM9 H61 NAG H61 "Carbohydrate core" 27 NM9 H62 NAG H62 "Carbohydrate core" 28 NM9 H4 NAG H4 "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 NM9 "CARBOHYDRATE ISOMER" D PDB ? NM9 "CARBOHYDRATE RING" pyranose PDB ? NM9 "CARBOHYDRATE ANOMER" beta PDB ? NM9 "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 NM9 "Create component" 2013-11-19 EBI NM9 "Initial release" 2014-07-23 RCSB NM9 "Other modification" 2014-07-24 EBI NM9 "Other modification" 2020-07-03 RCSB NM9 "Modify parent residue" 2020-07-17 RCSB NM9 "Modify name" 2020-07-17 RCSB NM9 "Modify synonyms" 2020-07-17 RCSB NM9 "Modify linking type" 2020-07-17 RCSB NM9 "Modify atom id" 2020-07-17 RCSB NM9 "Modify component atom id" 2020-07-17 RCSB NM9 "Modify leaving atom flag" 2020-07-17 RCSB ##