data_NBG
#
_chem_comp.id NBG
_chem_comp.name N-acetyl-beta-D-glucopyranosylamine
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C8 H15 N O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"1-N-ACETYL-BETA-D-GLUCOSAMINE; N-acetyl-beta-D-glucosylamine; N-acetyl-D-glucosylamine; N-acetyl-glucosylamine"
_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 NBG
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2PRJ
_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 NBG 1-N-ACETYL-BETA-D-GLUCOSAMINE PDB ?
2 NBG N-acetyl-beta-D-glucosylamine PDB ?
3 NBG N-acetyl-D-glucosylamine PDB ?
4 NBG N-acetyl-glucosylamine 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
NBG C1 C1 C 0 1 N N R N N N 33.936 22.776 27.763 0.279 0.034 0.698 C1 NBG 1
NBG C2 C2 C 0 1 N N R N N N 33.951 23.093 26.273 1.536 -0.311 -0.104 C2 NBG 2
NBG C3 C3 C 0 1 N N S N N N 32.663 22.566 25.616 1.407 0.281 -1.512 C3 NBG 3
NBG C4 C4 C 0 1 N N S N N N 32.443 21.100 25.979 0.088 -0.201 -2.127 C4 NBG 4
NBG C5 C5 C 0 1 N N R N N N 32.354 20.962 27.539 -1.058 0.134 -1.171 C5 NBG 5
NBG C6 C6 C 0 1 N N N N N N 32.148 19.535 27.933 -2.383 -0.313 -1.792 C6 NBG 6
NBG C7 C7 C 0 1 N N N N N N 35.581 23.636 29.291 -0.194 0.128 3.086 C7 NBG 7
NBG C8 C8 C 0 1 N N N N N N 37.103 23.837 29.569 -0.061 -0.419 4.484 C8 NBG 8
NBG N1 N1 N 0 1 N N N N N N 35.279 23.030 28.147 0.408 -0.498 2.057 N1 NBG 9
NBG O3 O3 O 0 1 N N N N N N 32.760 22.694 24.207 2.501 -0.155 -2.321 O3 NBG 10
NBG O2 O2 O 0 1 N N N N N N 34.052 24.482 26.097 2.684 0.240 0.543 O2 NBG 11
NBG O4 O4 O 0 1 N N N N N N 31.283 20.651 25.348 -0.124 0.453 -3.379 O4 NBG 12
NBG O5 O5 O 0 1 N N N N N N 33.582 21.399 28.109 -0.865 -0.538 0.070 O5 NBG 13
NBG O6 O6 O 0 1 N N N N N N 33.212 18.796 27.376 -3.457 0.004 -0.905 O6 NBG 14
NBG O7 O7 O 0 1 N N N N N N 34.726 24.019 30.099 -0.842 1.134 2.888 O7 NBG 15
NBG H1 H1 H 0 1 N N N N N N 33.154 23.382 28.278 0.164 1.117 0.743 H1 NBG 16
NBG H2 H2 H 0 1 N N N N N N 34.826 22.597 25.792 1.641 -1.394 -0.172 H2 NBG 17
NBG H3 H3 H 0 1 N N N N N N 31.799 23.164 25.989 1.407 1.369 -1.453 H3 NBG 18
NBG H4 H4 H 0 1 N N N N N N 33.294 20.470 25.630 0.130 -1.279 -2.281 H4 NBG 19
NBG H5 H5 H 0 1 N N N N N N 31.496 21.575 27.901 -1.084 1.210 -1.000 H5 NBG 20
NBG H61 H61 H 0 1 N N N N N N 32.046 19.394 29.034 -2.532 0.200 -2.742 H61 NBG 21
NBG H62 H62 H 0 1 N N N N N N 31.144 19.142 27.646 -2.359 -1.390 -1.961 H62 NBG 22
NBG H81 H81 H 0 1 N N N N N N 37.356 24.345 30.528 -0.612 0.216 5.177 H81 NBG 23
NBG H82 H82 H 0 1 N N N N N N 37.633 22.858 29.505 -0.468 -1.430 4.517 H82 NBG 24
NBG H83 H83 H 0 1 N N N N N N 37.577 24.376 28.716 0.990 -0.441 4.768 H83 NBG 25
NBG HN1 HN1 H 0 1 N N N N N N 36.073 22.761 27.566 0.926 -1.303 2.215 HN1 NBG 26
NBG HO3 HO3 H 0 1 N Y N N N N 31.964 22.368 23.801 3.308 0.168 -1.898 HO3 NBG 27
NBG HO2 HO2 H 0 1 N Y N N N N 34.061 24.679 25.167 2.727 -0.157 1.423 HO2 NBG 28
NBG HO4 HO4 H 0 1 N Y N N N N 31.146 19.738 25.574 0.619 0.215 -3.949 HO4 NBG 29
NBG HO6 HO6 H 0 1 N Y N N N N 33.081 17.889 27.626 -4.271 -0.293 -1.333 HO6 NBG 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
NBG C1 C2 SING N N 1
NBG C1 N1 SING N N 2
NBG C1 O5 SING N N 3
NBG C1 H1 SING N N 4
NBG C2 C3 SING N N 5
NBG C2 O2 SING N N 6
NBG C2 H2 SING N N 7
NBG C3 C4 SING N N 8
NBG C3 O3 SING N N 9
NBG C3 H3 SING N N 10
NBG C4 C5 SING N N 11
NBG C4 O4 SING N N 12
NBG C4 H4 SING N N 13
NBG C5 C6 SING N N 14
NBG C5 O5 SING N N 15
NBG C5 H5 SING N N 16
NBG C6 O6 SING N N 17
NBG C6 H61 SING N N 18
NBG C6 H62 SING N N 19
NBG C7 C8 SING N N 20
NBG C7 N1 SING N N 21
NBG C7 O7 DOUB N N 22
NBG C8 H81 SING N N 23
NBG C8 H82 SING N N 24
NBG C8 H83 SING N N 25
NBG N1 HN1 SING N N 26
NBG O3 HO3 SING N N 27
NBG O2 HO2 SING N N 28
NBG O4 HO4 SING N N 29
NBG 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
NBG SMILES ACDLabs 10.04 O=C(NC1OC(C(O)C(O)C1O)CO)C
NBG SMILES_CANONICAL CACTVS 3.341 CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
NBG SMILES CACTVS 3.341 CC(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
NBG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)N[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
NBG SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)NC1C(C(C(C(O1)CO)O)O)O
NBG InChI InChI 1.03 InChI=1S/C8H15NO6/c1-3(11)9-8-7(14)6(13)5(12)4(2-10)15-8/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8-/m1/s1
NBG InChIKey InChI 1.03 IBONACLSSOLHFU-JAJWTYFOSA-N
#
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
NBG "SYSTEMATIC NAME" ACDLabs 10.04 N-acetyl-beta-D-glucopyranosylamine
NBG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 N-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]ethanamide
NBG "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Glcp1NAc
#
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
NBG "CARBOHYDRATE ISOMER" D PDB ?
NBG "CARBOHYDRATE RING" pyranose PDB ?
NBG "CARBOHYDRATE ANOMER" beta PDB ?
NBG "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
NBG 'Create component' 1999-07-08 RCSB
NBG 'Modify descriptor' 2011-06-04 RCSB
NBG 'Other modification' 2020-07-03 RCSB
NBG 'Modify name' 2020-07-17 RCSB
NBG 'Modify synonyms' 2020-07-17 RCSB
NBG 'Modify linking type' 2020-07-17 RCSB
NBG 'Modify leaving atom flag' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id NBG
_pdbe_chem_comp_drugbank_details.drugbank_id DB02320
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name N-beta-D-glucopyranosylacetamide
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 6983-36-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
NBG 1-N-ACETYL-BETA-D-GLUCOSAMINE wwPDB ?
NBG N-acetyl-beta-D-glucosylamine wwPDB ?
NBG N-acetyl-D-glucosylamine wwPDB ?
NBG N-acetyl-glucosylamine wwPDB ?
NBG 1-N-acetyl-beta-D-glucosamine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id NBG
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02320
_pdbe_chem_comp_drugbank_classification.parent Hexoses
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.'
#
_pdbe_chem_comp_drugbank_targets.comp_id NBG
_pdbe_chem_comp_drugbank_targets.drugbank_id DB02320
_pdbe_chem_comp_drugbank_targets.name 'Glycogen phosphorylase, muscle form'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P11217
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
NBG C1 C 7.702 0.608 1
NBG C2 C 7.702 -0.892 2
NBG C3 C 6.404 -1.643 3
NBG C4 C 5.104 -0.892 4
NBG C5 C 5.104 0.608 5
NBG C6 C 3.805 1.357 6
NBG C7 C 9.002 2.857 7
NBG C8 C 7.702 3.607 8
NBG N1 N 9.002 1.357 9
NBG O3 O 6.404 -3.143 10
NBG O2 O 9.002 -1.643 11
NBG O4 O 3.805 -1.643 12
NBG O5 O 6.404 1.357 13
NBG O6 O 3.805 2.857 14
NBG O7 O 10.301 3.607 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
NBG C1 C2 SINGLE NONE 1
NBG C1 N1 SINGLE BEGINWEDGE 2
NBG C1 O5 SINGLE NONE 3
NBG C2 C3 SINGLE NONE 4
NBG C2 O2 SINGLE BEGINDASH 5
NBG C3 C4 SINGLE NONE 6
NBG C3 O3 SINGLE BEGINWEDGE 7
NBG C4 C5 SINGLE NONE 8
NBG C4 O4 SINGLE BEGINDASH 9
NBG C5 C6 SINGLE BEGINWEDGE 10
NBG C5 O5 SINGLE NONE 11
NBG C6 O6 SINGLE NONE 12
NBG C7 C8 SINGLE NONE 13
NBG C7 N1 SINGLE NONE 14
NBG 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
NBG MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
NBG amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
NBG C1 S1 1
NBG C2 S1 1
NBG C3 S1 1
NBG C4 S1 1
NBG C5 S1 1
NBG O5 S1 1
NBG N1 F1 1
NBG C7 F1 1
NBG O7 F1 1
NBG C8 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NBG
_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 1.307
_pdbe_chem_comp_rdkit_properties.chi3v 1.307
_pdbe_chem_comp_rdkit_properties.chi4v 0.726
_pdbe_chem_comp_rdkit_properties.chi0n 21.897
_pdbe_chem_comp_rdkit_properties.chi1n 10.456
_pdbe_chem_comp_rdkit_properties.chi2n 1.307
_pdbe_chem_comp_rdkit_properties.chi3n 1.307
_pdbe_chem_comp_rdkit_properties.chi4n 0.726
_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
NBG UniChem ChEMBL CHEMBL335315
NBG UniChem DrugBank DB02320
NBG UniChem PDBe NBG
NBG UniChem SureChEMBL SCHEMBL4388634
NBG UniChem BindingDb 50240802
NBG UniChem 'Probes And Drugs' PD060163
NBG UniChem Nikkaji J687.948I
NBG UniChem 'PubChem TPHARMA' 15948367
NBG UniChem PubChem 445382
#
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
NBG C1 0.708 -0.223 0.043 ETKDGv3 1
NBG C2 0.306 1.189 0.520 ETKDGv3 2
NBG C3 -1.156 1.191 0.999 ETKDGv3 3
NBG C4 -2.065 0.558 -0.073 ETKDGv3 4
NBG C5 -1.483 -0.809 -0.512 ETKDGv3 5
NBG C6 -2.320 -1.439 -1.639 ETKDGv3 6
NBG C7 3.223 -0.534 0.305 ETKDGv3 7
NBG C8 4.593 -0.376 -0.270 ETKDGv3 8
NBG N1 2.074 -0.188 -0.481 ETKDGv3 9
NBG O3 -1.555 2.513 1.252 ETKDGv3 10
NBG O2 1.164 1.647 1.536 ETKDGv3 11
NBG O4 -3.355 0.380 0.454 ETKDGv3 12
NBG O5 -0.159 -0.648 -0.994 ETKDGv3 13
NBG O6 -3.594 -1.807 -1.184 ETKDGv3 14
NBG O7 3.090 -0.947 1.489 ETKDGv3 15
NBG H1 0.660 -0.942 0.894 ETKDGv3 16
NBG H2 0.395 1.887 -0.343 ETKDGv3 17
NBG H3 -1.224 0.584 1.934 ETKDGv3 18
NBG H4 -2.099 1.230 -0.965 ETKDGv3 19
NBG H5 -1.496 -1.518 0.349 ETKDGv3 20
NBG H61 -1.792 -2.333 -2.043 ETKDGv3 21
NBG H62 -2.431 -0.717 -2.476 ETKDGv3 22
NBG H81 4.832 0.704 -0.361 ETKDGv3 23
NBG H82 5.349 -0.861 0.383 ETKDGv3 24
NBG H83 4.634 -0.846 -1.275 ETKDGv3 25
NBG HN1 2.227 0.217 -1.433 ETKDGv3 26
NBG HO3 -2.304 2.470 1.903 ETKDGv3 27
NBG HO2 1.095 1.012 2.297 ETKDGv3 28
NBG HO4 -3.840 1.237 0.331 ETKDGv3 29
NBG HO6 -3.476 -2.629 -0.640 ETKDGv3 30
#