data_AGL
#
_chem_comp.id AGL
_chem_comp.name 4-amino-4,6-dideoxy-alpha-D-glucopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H13 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE; 4-amino-4-deoxy-alpha-D-quinovopyranose; 4-amino-4,6-dideoxy-alpha-D-glucose;
4-amino-4,6-dideoxy-D-glucose; 4-amino-4,6-dideoxy-glucose
;
_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 163.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AGL
_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 1CPU
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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 AGL 4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE PDB ?
2 AGL 4-amino-4-deoxy-alpha-D-quinovopyranose PDB ?
3 AGL 4-amino-4,6-dideoxy-alpha-D-glucose PDB ?
4 AGL 4-amino-4,6-dideoxy-D-glucose PDB ?
5 AGL 4-amino-4,6-dideoxy-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.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
AGL C1 C1 C 0 1 N N S N N N 6.532 14.893 42.040 1.449 -0.221 -0.706 C1 AGL 1
AGL C2 C2 C 0 1 N N R N N N 6.858 14.615 43.538 0.098 -0.522 -1.360 C2 AGL 2
AGL C3 C3 C 0 1 N N S N N N 7.374 15.866 44.284 -1.006 0.189 -0.572 C3 AGL 3
AGL C4 C4 C 0 1 N N S N N N 8.495 16.520 43.441 -0.892 -0.211 0.902 C4 AGL 4
AGL C5 C5 C 0 1 N N R N N N 7.884 16.889 42.062 0.532 0.066 1.386 C5 AGL 5
AGL C6 C6 C 0 1 N N N N N N 8.903 17.657 41.210 0.647 -0.297 2.867 C6 AGL 6
AGL O1 O1 O 0 1 N Y N N N N 5.291 15.546 41.910 1.666 1.190 -0.693 O1 AGL 7
AGL O2 O2 O 0 1 N N N N N N 5.692 14.126 44.166 0.105 -0.051 -2.709 O2 AGL 8
AGL O3 O3 O 0 1 N N N N N N 7.902 15.456 45.526 -2.284 -0.199 -1.080 O3 AGL 9
AGL N4 N4 N 0 1 N N N N N N 8.999 17.748 44.102 -1.843 0.573 1.700 N4 AGL 10
AGL O5 O5 O 0 1 N N N N N N 7.514 15.682 41.384 1.458 -0.714 0.632 O5 AGL 11
AGL H1 H1 H 0 1 N N N N N N 6.508 13.889 41.554 2.243 -0.705 -1.275 H1 AGL 12
AGL H2 H2 H 0 1 N N N N N N 7.680 13.862 43.577 -0.080 -1.597 -1.349 H2 AGL 13
AGL H3 H3 H 0 1 N N N N N N 6.548 16.597 44.442 -0.888 1.268 -0.669 H3 AGL 14
AGL H4 H4 H 0 1 N N N N N N 9.350 15.813 43.328 -1.114 -1.273 1.010 H4 AGL 15
AGL H5 H5 H 0 1 N N N N N N 6.990 17.536 42.218 0.760 1.124 1.254 H5 AGL 16
AGL H61 H61 H 0 1 N N N N N N 8.464 17.922 40.219 1.662 -0.097 3.213 H61 AGL 17
AGL H62 H62 H 0 1 N N N N N N 9.295 18.554 41.742 -0.057 0.300 3.444 H62 AGL 18
AGL H63 H63 H 0 1 N N N N N N 9.860 17.095 41.102 0.420 -1.355 3.000 H63 AGL 19
AGL HO1 HO1 H 0 1 N Y N N N N 5.092 15.715 40.996 2.527 1.337 -0.279 HO1 AGL 20
AGL HO2 HO2 H 0 1 N Y N N N N 5.890 13.956 45.079 0.818 -0.519 -3.165 HO2 AGL 21
AGL HO3 HO3 H 0 1 N Y N N N N 8.219 16.225 45.984 -2.305 0.060 -2.011 HO3 AGL 22
AGL HN41 HN41 H 0 0 N N N N N N 9.737 18.179 43.546 -1.732 0.276 2.658 HN41 AGL 23
AGL HN42 HN42 H 0 0 N N N N N N 9.302 17.565 45.058 -1.536 1.533 1.657 HN42 AGL 24
#
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
AGL C1 C2 SING N N 1
AGL C1 O1 SING N N 2
AGL C1 O5 SING N N 3
AGL C1 H1 SING N N 4
AGL C2 C3 SING N N 5
AGL C2 O2 SING N N 6
AGL C2 H2 SING N N 7
AGL C3 C4 SING N N 8
AGL C3 O3 SING N N 9
AGL C3 H3 SING N N 10
AGL C4 C5 SING N N 11
AGL C4 N4 SING N N 12
AGL C4 H4 SING N N 13
AGL C5 C6 SING N N 14
AGL C5 O5 SING N N 15
AGL C5 H5 SING N N 16
AGL C6 H61 SING N N 17
AGL C6 H62 SING N N 18
AGL C6 H63 SING N N 19
AGL O1 HO1 SING N N 20
AGL O2 HO2 SING N N 21
AGL O3 HO3 SING N N 22
AGL N4 HN41 SING N N 23
AGL N4 HN42 SING N N 24
#
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
AGL SMILES ACDLabs 10.04 OC1C(N)C(OC(O)C1O)C
AGL SMILES_CANONICAL CACTVS 3.341 C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1N
AGL SMILES CACTVS 3.341 C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N
AGL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)N
AGL SMILES "OpenEye OEToolkits" 1.5.0 CC1C(C(C(C(O1)O)O)O)N
AGL InChI InChI 1.03 InChI=1S/C6H13NO4/c1-2-3(7)4(8)5(9)6(10)11-2/h2-6,8-10H,7H2,1H3/t2-,3-,4+,5-,6+/m1/s1
AGL InChIKey InChI 1.03 RJKBJEZZABBYBA-DVKNGEFBSA-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
AGL "SYSTEMATIC NAME" ACDLabs 10.04 4-amino-4,6-dideoxy-alpha-D-glucopyranose
AGL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3R,4S,5S,6R)-5-amino-6-methyl-oxane-2,3,4-triol
AGL "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DQuip[4N]a
AGL "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-6-deoxy-Glcp4N
#
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
AGL "CARBOHYDRATE ISOMER" D PDB ?
AGL "CARBOHYDRATE RING" pyranose PDB ?
AGL "CARBOHYDRATE ANOMER" alpha PDB ?
AGL "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
AGL 'Create component' 1999-07-08 PDBJ
AGL 'Modify descriptor' 2011-06-04 RCSB
AGL 'Other modification' 2020-07-03 RCSB
AGL 'Modify name' 2020-07-17 RCSB
AGL 'Modify synonyms' 2020-07-17 RCSB
AGL 'Modify linking type' 2020-07-17 RCSB
AGL 'Modify leaving atom flag' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id AGL
_pdbe_chem_comp_drugbank_details.drugbank_id DB03439
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 4,6-dideoxy-4-amino-alpha-D-glucose
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_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
AGL 4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE wwPDB ?
AGL 4-amino-4-deoxy-alpha-D-quinovopyranose wwPDB ?
AGL 4-amino-4,6-dideoxy-alpha-D-glucose wwPDB ?
AGL 4-amino-4,6-dideoxy-D-glucose wwPDB ?
AGL 4-amino-4,6-dideoxy-glucose wwPDB ?
AGL 4,6-dideoxy-4-amino-alpha-D-glucose DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id AGL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03439
_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 AGL
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03439
_pdbe_chem_comp_drugbank_targets.name 'Pancreatic alpha-amylase'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P04746
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
AGL C1 C 5.104 1.268 1
AGL C2 C 5.104 -0.233 2
AGL C3 C 6.404 -0.983 3
AGL C4 C 7.702 -0.233 4
AGL C5 C 7.702 1.268 5
AGL C6 C 9.002 2.018 6
AGL O1 O 3.805 2.018 7
AGL O2 O 3.805 -0.983 8
AGL O3 O 6.404 -2.482 9
AGL N4 N 9.002 -0.983 10
AGL O5 O 6.404 2.018 11
#
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
AGL C1 C2 SINGLE NONE 1
AGL C1 O1 SINGLE BEGINWEDGE 2
AGL C1 O5 SINGLE NONE 3
AGL C2 C3 SINGLE NONE 4
AGL C2 O2 SINGLE BEGINWEDGE 5
AGL C3 C4 SINGLE NONE 6
AGL C3 O3 SINGLE BEGINDASH 7
AGL C4 C5 SINGLE NONE 8
AGL C4 N4 SINGLE BEGINWEDGE 9
AGL C5 C6 SINGLE BEGINDASH 10
AGL C5 O5 SINGLE NONE 11
#
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
AGL MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
AGL pyranose F1 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
AGL C1 S1 1
AGL C2 S1 1
AGL C3 S1 1
AGL C4 S1 1
AGL C5 S1 1
AGL O5 S1 1
AGL C4 F1 1
AGL C5 F1 1
AGL O5 F1 1
AGL C1 F1 1
AGL C2 F1 1
AGL C3 F1 1
AGL O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AGL
_pdbe_chem_comp_rdkit_properties.exactmw 163.084
_pdbe_chem_comp_rdkit_properties.amw 163.173
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 83.035
_pdbe_chem_comp_rdkit_properties.tpsa 95.940
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.227
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.543
_pdbe_chem_comp_rdkit_properties.chi0v 5.080
_pdbe_chem_comp_rdkit_properties.chi1v 2.494
_pdbe_chem_comp_rdkit_properties.chi2v 1.017
_pdbe_chem_comp_rdkit_properties.chi3v 1.017
_pdbe_chem_comp_rdkit_properties.chi4v 0.491
_pdbe_chem_comp_rdkit_properties.chi0n 18.080
_pdbe_chem_comp_rdkit_properties.chi1n 8.613
_pdbe_chem_comp_rdkit_properties.chi2n 1.017
_pdbe_chem_comp_rdkit_properties.chi3n 1.017
_pdbe_chem_comp_rdkit_properties.chi4n 0.491
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.831
_pdbe_chem_comp_rdkit_properties.kappa2 3.040
_pdbe_chem_comp_rdkit_properties.kappa3 1.521
_pdbe_chem_comp_rdkit_properties.Phi 0.506
#
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
AGL UniChem DrugBank DB03439
AGL UniChem SureChEMBL SCHEMBL1543515
AGL UniChem 'Probes And Drugs' PD059637
AGL UniChem PubChem 444139
#
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
AGL C1 0.811 -1.159 -0.942 ETKDGv3 1
AGL C2 1.639 0.104 -0.619 ETKDGv3 2
AGL C3 0.915 1.001 0.415 ETKDGv3 3
AGL C4 -0.610 0.780 0.360 ETKDGv3 4
AGL C5 -0.918 -0.734 0.599 ETKDGv3 5
AGL C6 -2.229 -1.171 -0.066 ETKDGv3 6
AGL O1 1.655 -2.174 -1.416 ETKDGv3 7
AGL O2 2.901 -0.262 -0.122 ETKDGv3 8
AGL O3 1.226 2.347 0.148 ETKDGv3 9
AGL N4 -1.279 1.602 1.373 ETKDGv3 10
AGL O5 0.139 -1.612 0.219 ETKDGv3 11
AGL H1 0.082 -0.914 -1.750 ETKDGv3 12
AGL H2 1.769 0.663 -1.577 ETKDGv3 13
AGL H3 1.268 0.717 1.437 ETKDGv3 14
AGL H4 -0.970 1.084 -0.651 ETKDGv3 15
AGL H5 -1.054 -0.879 1.694 ETKDGv3 16
AGL H61 -2.192 -1.011 -1.164 ETKDGv3 17
AGL H62 -2.407 -2.250 0.128 ETKDGv3 18
AGL H63 -3.085 -0.598 0.348 ETKDGv3 19
AGL HO1 1.065 -2.923 -1.694 ETKDGv3 20
AGL HO2 3.477 0.545 -0.182 ETKDGv3 21
AGL HO3 1.273 2.816 1.022 ETKDGv3 22
AGL HN41 -2.307 1.417 1.327 ETKDGv3 23
AGL HN42 -1.168 2.608 1.111 ETKDGv3 24
#