data_NOJ
#
_chem_comp.id NOJ
_chem_comp.name 1-DEOXYNOJIRIMYCIN
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H13 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms MORANOLINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-08-16
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces DNJ
_chem_comp.formula_weight 163.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NOJ
_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 1DOG
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
NOJ C1 C1 C 0 1 N N N N N N 31.502 17.462 4.219 -0.567 -1.798 -0.192 C1 NOJ 1
NOJ C2 C2 C 0 1 N N S N N N 32.509 17.825 5.325 -1.616 -0.787 0.276 C2 NOJ 2
NOJ O2 O2 O 0 1 N N N N N N 31.817 18.616 6.325 -2.899 -1.162 -0.231 O2 NOJ 3
NOJ C3 C3 C 0 1 N N R N N N 33.716 18.643 4.860 -1.246 0.604 -0.247 C3 NOJ 4
NOJ O3 O3 O 0 1 N N N N N N 34.814 18.602 5.795 -2.191 1.562 0.234 O3 NOJ 5
NOJ C4 C4 C 0 1 N N R N N N 34.228 18.111 3.507 0.154 0.972 0.252 C4 NOJ 6
NOJ O4 O4 O 0 1 N N N N N N 35.335 18.918 3.067 0.530 2.245 -0.278 O4 NOJ 7
NOJ C5 C5 C 0 1 N N R N N N 33.091 18.162 2.473 1.152 -0.090 -0.215 C5 NOJ 8
NOJ N5 N5 N 0 1 N N N N N N 31.959 17.453 2.914 0.755 -1.402 0.311 N5 NOJ 9
NOJ C6 C6 C 0 1 N N N N N N 33.518 17.562 1.100 2.550 0.263 0.298 C6 NOJ 10
NOJ O6 O6 O 0 1 N N N N N N 33.243 18.503 0.046 3.500 -0.663 -0.234 O6 NOJ 11
NOJ H11 H11 H 0 1 N N N N N N 31.141 16.446 4.437 -0.820 -2.787 0.191 H11 NOJ 12
NOJ H12 H12 H 0 1 N N N N N N 30.693 18.205 4.268 -0.548 -1.824 -1.281 H12 NOJ 13
NOJ H2 H2 H 0 1 N N N N N N 32.898 16.868 5.703 -1.646 -0.771 1.365 H2 NOJ 14
NOJ HO2 HO2 H 0 1 N N N N N N 32.423 18.851 7.018 -3.196 -2.035 0.058 HO2 NOJ 15
NOJ H3 H3 H 0 1 N N N N N N 33.367 19.683 4.775 -1.256 0.598 -1.337 H3 NOJ 16
NOJ HO3 HO3 H 0 1 N N N N N N 35.535 19.123 5.461 -3.102 1.387 -0.040 HO3 NOJ 17
NOJ H4 H4 H 0 1 N N N N N N 34.563 17.069 3.618 0.153 1.017 1.341 H4 NOJ 18
NOJ HO4 HO4 H 0 1 N N N N N N 35.653 18.593 2.233 -0.062 2.966 -0.024 HO4 NOJ 19
NOJ H5 H5 H 0 1 N N N N N N 32.850 19.228 2.352 1.163 -0.124 -1.305 H5 NOJ 20
NOJ HN5 HN5 H 0 1 N N N N N N 32.165 16.494 2.720 0.774 -1.408 1.320 HN5 NOJ 21
NOJ H61 H61 H 0 1 N N N N N N 34.595 17.341 1.119 2.809 1.273 -0.020 H61 NOJ 22
NOJ H62 H62 H 0 1 N N N N N N 32.954 16.635 0.917 2.561 0.211 1.386 H62 NOJ 23
NOJ HO6 HO6 H 0 1 N N N N N N 33.506 18.131 -0.788 4.410 -0.499 0.050 HO6 NOJ 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
NOJ C1 C2 SING N N 1
NOJ C1 N5 SING N N 2
NOJ C1 H11 SING N N 3
NOJ C1 H12 SING N N 4
NOJ C2 O2 SING N N 5
NOJ C2 C3 SING N N 6
NOJ C2 H2 SING N N 7
NOJ O2 HO2 SING N N 8
NOJ C3 O3 SING N N 9
NOJ C3 C4 SING N N 10
NOJ C3 H3 SING N N 11
NOJ O3 HO3 SING N N 12
NOJ C4 O4 SING N N 13
NOJ C4 C5 SING N N 14
NOJ C4 H4 SING N N 15
NOJ O4 HO4 SING N N 16
NOJ C5 N5 SING N N 17
NOJ C5 C6 SING N N 18
NOJ C5 H5 SING N N 19
NOJ N5 HN5 SING N N 20
NOJ C6 O6 SING N N 21
NOJ C6 H61 SING N N 22
NOJ C6 H62 SING N N 23
NOJ O6 HO6 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
NOJ SMILES ACDLabs 12.01 OC1C(NCC(O)C1O)CO
NOJ SMILES_CANONICAL CACTVS 3.370 OC[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O
NOJ SMILES CACTVS 3.370 OC[CH]1NC[CH](O)[CH](O)[CH]1O
NOJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C1[C@@H]([C@H]([C@@H]([C@H](N1)CO)O)O)O
NOJ SMILES "OpenEye OEToolkits" 1.7.0 C1C(C(C(C(N1)CO)O)O)O
NOJ InChI InChI 1.03 InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5-,6-/m1/s1
NOJ InChIKey InChI 1.03 LXBIFEVIBLOUGU-JGWLITMVSA-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
NOJ "SYSTEMATIC NAME" ACDLabs 12.01 (2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
NOJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 (2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
#
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
NOJ "CARBOHYDRATE ISOMER" D PDB ?
NOJ "CARBOHYDRATE RING" pyranose 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
NOJ 'Create component' 1999-07-08 RCSB
NOJ 'Modify descriptor' 2011-06-04 RCSB
NOJ 'Modify synonyms' 2021-03-01 PDBE
NOJ 'Other modification' 2024-08-16 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id NOJ
_pdbx_chem_comp_synonyms.name MORANOLINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id NOJ
_pdbe_chem_comp_drugbank_details.drugbank_id DB03206
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Duvoglustat
_pdbe_chem_comp_drugbank_details.description
'An alpha-glucosidase inhibitor with antiviral action. Derivatives of deoxynojirimycin may have anti-HIV activity.'
_pdbe_chem_comp_drugbank_details.cas_number 19130-96-2
_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
NOJ MORANOLINE wwPDB ?
NOJ (+)-1-Deoxynojirimycin DrugBank ?
NOJ '1 deoxynojirimycin' DrugBank ?
NOJ 1-deoxy-nojirimycin DrugBank ?
NOJ 1-deoxynojirimycin DrugBank ?
NOJ 1,5-deoxy-1,5-imino-D-mannitol DrugBank ?
NOJ 1,5-dideoxy-1,5-imino-D-glucitol DrugBank ?
NOJ 5-amino-1,5-dideoxy-D-glucopyranose DrugBank ?
NOJ D-1-deoxynojirimycin DrugBank ?
NOJ Deoxynojirimycin DrugBank ?
NOJ DNJ DrugBank ?
NOJ Duvoglustat DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id NOJ
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03206
_pdbe_chem_comp_drugbank_classification.parent Piperidines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Piperidines
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as piperidines. These are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
NOJ DB03206 'Cyclomaltodextrin glucanotransferase' 'Bacillus sp. (strain 1011)' P05618 unknown 1
NOJ DB03206 'Beta-glucosidase A' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q08638 unknown 2
NOJ DB03206 'Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase' Humans Q9UKM7 unknown 3
NOJ DB03206 'Mannosyl-oligosaccharide alpha-1,2-mannosidase' 'Penicillium citrinum' P31723 unknown 4
NOJ DB03206 'Xylose isomerase' 'Arthrobacter sp. (strain NRRL B3728)' P12070 unknown 5
#
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
NOJ C1 C 5.104 -0.750 1
NOJ C2 C 5.104 0.750 2
NOJ O2 O 3.805 1.500 3
NOJ C3 C 6.404 1.500 4
NOJ O3 O 6.404 3.000 5
NOJ C4 C 7.702 0.750 6
NOJ O4 O 9.002 1.500 7
NOJ C5 C 7.702 -0.750 8
NOJ N5 N 6.404 -1.500 9
NOJ C6 C 9.002 -1.500 10
NOJ O6 O 9.002 -3.000 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
NOJ C1 C2 SINGLE NONE 1
NOJ C1 N5 SINGLE NONE 2
NOJ C2 O2 SINGLE BEGINDASH 3
NOJ C2 C3 SINGLE NONE 4
NOJ C3 O3 SINGLE BEGINWEDGE 5
NOJ C3 C4 SINGLE NONE 6
NOJ C4 O4 SINGLE BEGINDASH 7
NOJ C4 C5 SINGLE NONE 8
NOJ C5 N5 SINGLE NONE 9
NOJ C5 C6 SINGLE BEGINWEDGE 10
NOJ C6 O6 SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id NOJ
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCNCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys NQRYJNQNLNOLGT-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
NOJ C1 S1 1
NOJ C2 S1 1
NOJ C3 S1 1
NOJ C4 S1 1
NOJ C5 S1 1
NOJ N5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NOJ
_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 5
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 82.954
_pdbe_chem_comp_rdkit_properties.tpsa 92.950
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.967
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.897
_pdbe_chem_comp_rdkit_properties.chi0v 5.080
_pdbe_chem_comp_rdkit_properties.chi1v 2.514
_pdbe_chem_comp_rdkit_properties.chi2v 0.993
_pdbe_chem_comp_rdkit_properties.chi3v 0.993
_pdbe_chem_comp_rdkit_properties.chi4v 0.488
_pdbe_chem_comp_rdkit_properties.chi0n 18.080
_pdbe_chem_comp_rdkit_properties.chi1n 8.594
_pdbe_chem_comp_rdkit_properties.chi2n 0.993
_pdbe_chem_comp_rdkit_properties.chi3n 0.993
_pdbe_chem_comp_rdkit_properties.chi4n 0.488
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.831
_pdbe_chem_comp_rdkit_properties.kappa2 3.465
_pdbe_chem_comp_rdkit_properties.kappa3 1.687
_pdbe_chem_comp_rdkit_properties.Phi 0.577
#
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
NOJ UniChem ChEMBL CHEMBL307429
NOJ UniChem DrugBank DB03206
NOJ UniChem PDBe NOJ
NOJ UniChem 'Guide to Pharmacology' 4642
NOJ UniChem 'KEGG LIGAND' C16843
NOJ UniChem ChEBI 44369
NOJ UniChem ZINC ZINC000003794714
NOJ UniChem eMolecules 1934747
NOJ UniChem fdasrs FZ56898FLE
NOJ UniChem NMRShiftDB 60062487
NOJ UniChem ACTor 19130-96-2
NOJ UniChem Nikkaji J261.805B
NOJ UniChem BindingDb 18351
NOJ UniChem 'EPA CompTox Dashboard' DTXSID70172647
NOJ UniChem MetaboLights MTBLC44369
NOJ UniChem BRENDA 1922
NOJ UniChem BRENDA 50691
NOJ UniChem BRENDA 557
NOJ UniChem BRENDA 65073
NOJ UniChem ChemicalBook CB9128150
NOJ UniChem ClinicalTrials 1-DEOXYNOJIRIMYCIN
NOJ UniChem ClinicalTrials AT-2220
NOJ UniChem ClinicalTrials AT2220
NOJ UniChem ClinicalTrials DUVOGLUSTAT
NOJ UniChem ClinicalTrials 'DUVOGLUSTAT HYDROCHLORIDE'
NOJ UniChem MedChemExpress HY-14860
NOJ UniChem 'Probes And Drugs' PD016126
NOJ UniChem SureChEMBL SCHEMBL2969
NOJ UniChem 'PubChem TPHARMA' 15219397
NOJ UniChem 'PubChem TPHARMA' 15219399
NOJ UniChem PubChem 29435
#
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
NOJ C1 -1.443 -0.961 -0.804 ETKDGv3 1
NOJ C2 -1.271 -0.763 0.708 ETKDGv3 2
NOJ O2 -2.503 -0.945 1.358 ETKDGv3 3
NOJ C3 -0.729 0.650 1.026 ETKDGv3 4
NOJ O3 0.084 0.578 2.171 ETKDGv3 5
NOJ C4 0.062 1.272 -0.155 ETKDGv3 6
NOJ O4 -0.824 2.010 -0.961 ETKDGv3 7
NOJ C5 0.771 0.193 -1.021 ETKDGv3 8
NOJ N5 -0.162 -0.848 -1.525 ETKDGv3 9
NOJ C6 1.986 -0.430 -0.297 ETKDGv3 10
NOJ O6 2.920 0.563 0.029 ETKDGv3 11
NOJ H11 -1.884 -1.964 -0.996 ETKDGv3 12
NOJ H12 -2.160 -0.214 -1.207 ETKDGv3 13
NOJ H2 -0.547 -1.528 1.076 ETKDGv3 14
NOJ HO2 -2.680 -1.923 1.372 ETKDGv3 15
NOJ H3 -1.598 1.316 1.247 ETKDGv3 16
NOJ HO3 0.148 1.498 2.540 ETKDGv3 17
NOJ H4 0.821 1.977 0.259 ETKDGv3 18
NOJ HO4 -0.272 2.624 -1.514 ETKDGv3 19
NOJ H5 1.184 0.712 -1.915 ETKDGv3 20
NOJ HN5 0.298 -1.789 -1.542 ETKDGv3 21
NOJ H61 1.665 -0.961 0.623 ETKDGv3 22
NOJ H62 2.473 -1.170 -0.972 ETKDGv3 23
NOJ HO6 3.661 0.102 0.500 ETKDGv3 24
#