data_NAG # _chem_comp.id NAG _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H15 N O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 221.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NAG _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 8PCH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 NAG N-acetyl-beta-D-glucosamine PDB ? 2 NAG 2-acetamido-2-deoxy-beta-D-glucose PDB ? 3 NAG 2-acetamido-2-deoxy-D-glucose PDB ? 4 NAG 2-acetamido-2-deoxy-glucose PDB ? 5 NAG N-ACETYL-D-GLUCOSAMINE 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 NAG C1 C1 C 0 1 N N R N N N 7.396 28.163 26.662 0.185 1.082 -0.421 C1 NAG 1 NAG C2 C2 C 0 1 N N R N N N 6.973 29.233 27.644 0.790 -0.220 0.112 C2 NAG 2 NAG C3 C3 C 0 1 N N R N N N 7.667 29.055 29.000 -0.124 -1.390 -0.265 C3 NAG 3 NAG C4 C4 C 0 1 N N S N N N 7.573 27.588 29.490 -1.526 -1.129 0.294 C4 NAG 4 NAG C5 C5 C 0 1 N N R N N N 7.902 26.592 28.373 -2.042 0.207 -0.246 C5 NAG 5 NAG C6 C6 C 0 1 N N N N N N 7.599 25.173 28.797 -3.417 0.504 0.355 C6 NAG 6 NAG C7 C7 C 0 1 N N N N N N 6.291 31.299 26.595 3.197 0.157 0.076 C7 NAG 7 NAG C8 C8 C 0 1 N N N N N N 6.684 32.649 26.036 4.559 -0.052 -0.533 C8 NAG 8 NAG N2 N2 N 0 1 N N N N N N 7.268 30.545 27.089 2.114 -0.422 -0.480 N2 NAG 9 NAG O1 O1 O 0 1 N Y N N N N 6.676 28.363 25.419 1.003 2.185 -0.024 O1 NAG 10 NAG O3 O3 O 0 1 N N N N N N 7.038 29.909 29.947 0.395 -2.600 0.291 O3 NAG 11 NAG O4 O4 O 0 1 N N N N N N 8.494 27.358 30.574 -2.405 -2.180 -0.114 O4 NAG 12 NAG O5 O5 O 0 1 N N N N N N 7.104 26.875 27.206 -1.130 1.248 0.113 O5 NAG 13 NAG O6 O6 O 0 1 N N N N N N 6.232 25.040 29.165 -3.949 1.691 -0.236 O6 NAG 14 NAG O7 O7 O 0 1 N N N N N N 5.114 30.936 26.562 3.074 0.845 1.067 O7 NAG 15 NAG H1 H1 H 0 1 N N N N N N 8.477 28.257 26.481 0.133 1.040 -1.509 H1 NAG 16 NAG H2 H2 H 0 1 N N N N N N 5.888 29.146 27.803 0.879 -0.163 1.197 H2 NAG 17 NAG H3 H3 H 0 1 N N N N N N 8.729 29.321 28.892 -0.174 -1.478 -1.350 H3 NAG 18 NAG H4 H4 H 0 1 N N N N N N 6.544 27.403 29.831 -1.483 -1.091 1.382 H4 NAG 19 NAG H5 H5 H 0 1 N N N N N N 8.971 26.674 28.128 -2.123 0.154 -1.332 H5 NAG 20 NAG H61 H61 H 0 1 N N N N N N 7.816 24.492 27.961 -4.088 -0.333 0.157 H61 NAG 21 NAG H62 H62 H 0 1 N N N N N N 8.232 24.910 29.657 -3.320 0.645 1.431 H62 NAG 22 NAG H81 H81 H 0 1 N N N N N N 5.791 33.159 25.646 4.560 0.320 -1.558 H81 NAG 23 NAG H82 H82 H 0 1 N N N N N N 7.136 33.258 26.833 5.305 0.490 0.050 H82 NAG 24 NAG H83 H83 H 0 1 N N N N N N 7.411 32.511 25.222 4.799 -1.115 -0.532 H83 NAG 25 NAG HN2 HN2 H 0 1 N N N N N N 8.210 30.881 27.079 2.212 -0.973 -1.273 HN2 NAG 26 NAG HO1 HO1 H 0 1 N Y N N N N 6.933 27.696 24.793 0.679 3.044 -0.328 HO1 NAG 27 NAG HO3 HO3 H 0 1 N Y N N N N 7.459 29.809 30.793 -0.135 -3.384 0.091 HO3 NAG 28 NAG HO4 HO4 H 0 1 N Y N N N N 8.425 26.456 30.863 -3.312 -2.079 0.206 HO4 NAG 29 NAG HO6 HO6 H 0 1 N Y N N N N 6.060 24.143 29.428 -4.822 1.940 0.099 HO6 NAG 30 # 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 NAG C1 C2 SING N N 1 NAG C1 O1 SING N N 2 NAG C1 O5 SING N N 3 NAG C1 H1 SING N N 4 NAG C2 C3 SING N N 5 NAG C2 N2 SING N N 6 NAG C2 H2 SING N N 7 NAG C3 C4 SING N N 8 NAG C3 O3 SING N N 9 NAG C3 H3 SING N N 10 NAG C4 C5 SING N N 11 NAG C4 O4 SING N N 12 NAG C4 H4 SING N N 13 NAG C5 C6 SING N N 14 NAG C5 O5 SING N N 15 NAG C5 H5 SING N N 16 NAG C6 O6 SING N N 17 NAG C6 H61 SING N N 18 NAG C6 H62 SING N N 19 NAG C7 C8 SING N N 20 NAG C7 N2 SING N N 21 NAG C7 O7 DOUB N N 22 NAG C8 H81 SING N N 23 NAG C8 H82 SING N N 24 NAG C8 H83 SING N N 25 NAG N2 HN2 SING N N 26 NAG O1 HO1 SING N N 27 NAG O3 HO3 SING N N 28 NAG O4 HO4 SING N N 29 NAG O6 HO6 SING N N 30 # 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 NAG SMILES ACDLabs 12.01 O=C(NC1C(O)C(O)C(OC1O)CO)C NAG InChI InChI 1.03 InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1 NAG InChIKey InChI 1.03 OVRNDRQMDRJTHS-FMDGEEDCSA-N NAG SMILES_CANONICAL CACTVS 3.370 CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O NAG SMILES CACTVS 3.370 CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O NAG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O NAG SMILES "OpenEye OEToolkits" 1.7.6 CC(=O)NC1C(C(C(OC1O)CO)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 NAG "SYSTEMATIC NAME" ACDLabs 12.01 2-(acetylamino)-2-deoxy-beta-D-glucopyranose NAG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide NAG "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpNAcb NAG "COMMON NAME" GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-GlcpNAc NAG "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GlcNAc # 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 NAG "CARBOHYDRATE ISOMER" D PDB ? NAG "CARBOHYDRATE RING" pyranose PDB ? NAG "CARBOHYDRATE ANOMER" beta PDB ? NAG "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 NAG 'Create component' 1999-07-08 RCSB NAG 'Modify descriptor' 2011-06-04 RCSB NAG 'Modify leaving atom flag' 2011-07-01 RCSB NAG 'Modify leaving atom flag' 2012-11-26 RCSB NAG 'Other modification' 2019-08-12 RCSB NAG 'Other modification' 2019-12-19 RCSB NAG 'Other modification' 2020-07-03 RCSB NAG 'Modify name' 2020-07-17 RCSB NAG 'Modify synonyms' 2020-07-17 RCSB # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type NAG N-acetyl-beta-D-glucosamine wwPDB ? NAG 2-acetamido-2-deoxy-beta-D-glucose wwPDB ? NAG 2-acetamido-2-deoxy-D-glucose wwPDB ? NAG 2-acetamido-2-deoxy-glucose wwPDB ? NAG N-ACETYL-D-GLUCOSAMINE wwPDB ? # loop_ _software.name _software.version _software.description rdkit 2023.03.3 'Core functionality.' pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal NAG C1 C 7.702 0.750 1 NAG C2 C 7.702 -0.750 2 NAG C3 C 6.404 -1.500 3 NAG C4 C 5.104 -0.750 4 NAG C5 C 5.104 0.750 5 NAG C6 C 3.805 1.500 6 NAG C7 C 10.301 -0.750 7 NAG C8 C 10.301 0.750 8 NAG N2 N 9.002 -1.500 9 NAG O1 O 9.002 1.500 10 NAG O3 O 6.404 -3.000 11 NAG O4 O 3.805 -1.500 12 NAG O5 O 6.404 1.500 13 NAG O6 O 3.805 3.000 14 NAG O7 O 11.600 -1.500 15 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal NAG C1 C2 SINGLE NONE 1 NAG C1 O1 SINGLE BEGINWEDGE 2 NAG C1 O5 SINGLE NONE 3 NAG C2 C3 SINGLE NONE 4 NAG C2 N2 SINGLE BEGINDASH 5 NAG C3 C4 SINGLE NONE 6 NAG C3 O3 SINGLE BEGINWEDGE 7 NAG C4 C5 SINGLE NONE 8 NAG C4 O4 SINGLE BEGINDASH 9 NAG C5 C6 SINGLE BEGINWEDGE 10 NAG C5 O5 SINGLE NONE 11 NAG C6 O6 SINGLE NONE 12 NAG C7 C8 SINGLE NONE 13 NAG C7 N2 SINGLE NONE 14 NAG C7 O7 DOUBLE NONE 15 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys NAG MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N NAG amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N NAG pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal NAG C1 S1 1 NAG C2 S1 1 NAG C3 S1 1 NAG C4 S1 1 NAG C5 S1 1 NAG O5 S1 1 NAG N2 F1 1 NAG C7 F1 1 NAG O7 F1 1 NAG C8 F1 1 NAG C4 F2 1 NAG C5 F2 1 NAG O5 F2 1 NAG C1 F2 1 NAG C2 F2 1 NAG C3 F2 1 NAG O1 F2 1 # _pdbe_chem_comp_rdkit_properties.comp_id NAG _pdbe_chem_comp_rdkit_properties.exactmw 221.090 _pdbe_chem_comp_rdkit_properties.amw 221.209 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 7 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 6 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15 _pdbe_chem_comp_rdkit_properties.NumAtoms 30 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 1 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875 _pdbe_chem_comp_rdkit_properties.NumRings 1 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 107.769 _pdbe_chem_comp_rdkit_properties.tpsa 119.250 _pdbe_chem_comp_rdkit_properties.CrippenClogP -3.078 _pdbe_chem_comp_rdkit_properties.CrippenMR 47.584 _pdbe_chem_comp_rdkit_properties.chi0v 6.897 _pdbe_chem_comp_rdkit_properties.chi1v 3.376 _pdbe_chem_comp_rdkit_properties.chi2v 1.322 _pdbe_chem_comp_rdkit_properties.chi3v 1.322 _pdbe_chem_comp_rdkit_properties.chi4v 0.756 _pdbe_chem_comp_rdkit_properties.chi0n 21.897 _pdbe_chem_comp_rdkit_properties.chi1n 10.456 _pdbe_chem_comp_rdkit_properties.chi2n 1.322 _pdbe_chem_comp_rdkit_properties.chi3n 1.322 _pdbe_chem_comp_rdkit_properties.chi4n 0.756 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.730 _pdbe_chem_comp_rdkit_properties.kappa1 2.933 _pdbe_chem_comp_rdkit_properties.kappa2 4.862 _pdbe_chem_comp_rdkit_properties.kappa3 2.639 _pdbe_chem_comp_rdkit_properties.Phi 0.951 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id NAG UniChem ChEMBL CHEMBL447878 NAG UniChem PDBe NAG NAG UniChem 'KEGG LIGAND' C03878 NAG UniChem ChEBI 28009 NAG UniChem ZINC ZINC000003983907 NAG UniChem fdasrs 8P59336F68 NAG UniChem HMDB HMDB0000803 NAG UniChem 'PubChem TPHARMA' 14797954 NAG UniChem NMRShiftDB 60020515 NAG UniChem ACTor 134-61-2 NAG UniChem DrugCentral 4615 NAG UniChem MetaboLights MTBLC28009 NAG UniChem BRENDA 10471 NAG UniChem BRENDA 108031 NAG UniChem BRENDA 124708 NAG UniChem BRENDA 1507 NAG UniChem BRENDA 160963 NAG UniChem BRENDA 203758 NAG UniChem BRENDA 211749 NAG UniChem BRENDA 21317 NAG UniChem BRENDA 225422 NAG UniChem BRENDA 23245 NAG UniChem BRENDA 234335 NAG UniChem BRENDA 39369 NAG UniChem BRENDA 52462 NAG UniChem BRENDA 67193 NAG UniChem 'Probes And Drugs' PD001620 NAG UniChem BindingDb 50481442 NAG UniChem eMolecules 884266 NAG UniChem SureChEMBL SCHEMBL19345 NAG UniChem 'PubChem TPHARMA' 15121434 NAG UniChem PubChem 24139 NAG UniChem Nikkaji J419.924C # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal NAG C1 -0.008 1.027 0.658 ETKDGv3 1 NAG C2 0.782 -0.150 0.054 ETKDGv3 2 NAG C3 -0.080 -0.872 -0.995 ETKDGv3 3 NAG C4 -1.458 -1.218 -0.396 ETKDGv3 4 NAG C5 -2.083 0.040 0.261 ETKDGv3 5 NAG C6 -3.420 -0.304 0.928 ETKDGv3 6 NAG C7 3.304 0.219 0.059 ETKDGv3 7 NAG C8 4.507 0.814 -0.597 ETKDGv3 8 NAG N2 2.018 0.339 -0.565 ETKDGv3 9 NAG O1 0.774 1.640 1.647 ETKDGv3 10 NAG O3 0.576 -2.045 -1.404 ETKDGv3 11 NAG O4 -2.306 -1.754 -1.383 ETKDGv3 12 NAG O5 -1.209 0.561 1.249 ETKDGv3 13 NAG O6 -3.969 0.849 1.503 ETKDGv3 14 NAG O7 3.426 -0.359 1.173 ETKDGv3 15 NAG H1 -0.224 1.780 -0.140 ETKDGv3 16 NAG H2 1.016 -0.873 0.868 ETKDGv3 17 NAG H3 -0.219 -0.190 -1.869 ETKDGv3 18 NAG H4 -1.313 -1.992 0.390 ETKDGv3 19 NAG H5 -2.290 0.810 -0.520 ETKDGv3 20 NAG H61 -4.127 -0.708 0.169 ETKDGv3 21 NAG H62 -3.259 -1.075 1.715 ETKDGv3 22 NAG H81 5.437 0.457 -0.105 ETKDGv3 23 NAG H82 4.534 0.520 -1.667 ETKDGv3 24 NAG H83 4.459 1.920 -0.523 ETKDGv3 25 NAG HN2 1.946 0.902 -1.444 ETKDGv3 26 NAG HO1 0.280 2.452 1.932 ETKDGv3 27 NAG HO3 0.180 -2.306 -2.277 ETKDGv3 28 NAG HO4 -2.452 -1.051 -2.069 ETKDGv3 29 NAG HO6 -4.822 0.567 1.925 ETKDGv3 30 #