data_CGB
#
_chem_comp.id CGB
_chem_comp.name "CALYSTEGINE B2"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H13 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms (1S,2R,3S,4R,5S)-8-AZABICYCLO[3.2.1]OCTANE-1,2,3,4-TETROL
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-01-09
_chem_comp.pdbx_modified_date 2020-06-17
_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 175.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CGB
_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 2CBV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
CGB O2 O2 O 0 1 N N N N N N 0.589 12.877 10.418 -2.741 -0.002 -0.471 O2 CGB 1
CGB C2 C2 C 0 1 N N R N N N 0.047 11.645 9.945 -1.357 -0.211 -0.183 C2 CGB 2
CGB N1 N1 N 0 1 N N N N N N -1.044 11.199 10.787 -0.746 -1.234 -1.072 N1 CGB 3
CGB C8 C8 C 0 1 N N N N N N 1.012 10.468 10.059 -1.132 -0.747 1.249 C8 CGB 4
CGB C7 C7 C 0 1 N N N N N N 0.116 9.246 10.283 0.110 -1.656 1.140 C7 CGB 5
CGB C6 C6 C 0 1 N N R N N N -1.300 9.828 10.447 0.520 -1.589 -0.377 C6 CGB 6
CGB C3 C3 C 0 1 N N S N N N -0.454 11.763 8.488 -0.533 1.078 -0.338 C3 CGB 7
CGB O3 O3 O 0 1 N N N N N N 0.686 12.052 7.664 -1.132 2.126 0.426 O3 CGB 8
CGB C4 C4 C 0 1 N N R N N N -1.187 10.468 8.034 0.889 0.821 0.169 C4 CGB 9
CGB O4 O4 O 0 1 N N N N N N -1.936 10.699 6.843 1.701 1.966 -0.096 O4 CGB 10
CGB C5 C5 C 0 1 N N S N N N -2.092 9.896 9.128 1.479 -0.400 -0.543 C5 CGB 11
CGB O5 O5 O 0 1 N N N N N N -2.569 8.576 8.799 2.746 -0.723 0.033 O5 CGB 12
CGB HO HO H 0 1 N N N N N N 0.709 12.830 11.359 -3.183 -0.853 -0.351 HO CGB 13
CGB H1 H1 H 0 1 N N N N N N -0.793 11.277 11.752 -1.343 -2.047 -1.020 H1 CGB 14
CGB H8C1 1H8C H 0 0 N N N N N N 1.735 10.605 10.877 -0.940 0.077 1.937 H8C1 CGB 15
CGB H8C2 2H8C H 0 0 N N N N N N 1.609 10.357 9.142 -1.996 -1.323 1.579 H8C2 CGB 16
CGB H7C1 1H7C H 0 0 N N N N N N 0.427 8.658 11.159 0.912 -1.279 1.774 H7C1 CGB 17
CGB H7C2 2H7C H 0 0 N N N N N N 0.165 8.556 9.427 -0.144 -2.679 1.416 H7C2 CGB 18
CGB H6 H6 H 0 1 N N N N N N -1.873 9.218 11.160 0.947 -2.527 -0.730 H6 CGB 19
CGB H3 H3 H 0 1 N N N N N N -1.194 12.572 8.400 -0.499 1.365 -1.389 H3 CGB 20
CGB HA HA H 0 1 N N N N N N 0.413 12.116 6.756 -0.578 2.910 0.306 HA CGB 21
CGB H4 H4 H 0 1 N N N N N N -0.408 9.719 7.827 0.862 0.636 1.243 H4 CGB 22
CGB HB HB H 0 1 N N N N N N -2.861 10.750 7.055 2.585 1.765 0.241 HB CGB 23
CGB H5 H5 H 0 1 N N N N N N -2.966 10.557 9.226 1.606 -0.178 -1.603 H5 CGB 24
CGB HC HC H 0 1 N N N N N N -2.674 8.502 7.858 3.315 0.050 -0.090 HC CGB 25
#
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
CGB O2 C2 SING N N 1
CGB O2 HO SING N N 2
CGB C2 N1 SING N N 3
CGB C2 C8 SING N N 4
CGB C2 C3 SING N N 5
CGB N1 C6 SING N N 6
CGB N1 H1 SING N N 7
CGB C8 C7 SING N N 8
CGB C8 H8C1 SING N N 9
CGB C8 H8C2 SING N N 10
CGB C7 C6 SING N N 11
CGB C7 H7C1 SING N N 12
CGB C7 H7C2 SING N N 13
CGB C6 C5 SING N N 14
CGB C6 H6 SING N N 15
CGB C3 O3 SING N N 16
CGB C3 C4 SING N N 17
CGB C3 H3 SING N N 18
CGB O3 HA SING N N 19
CGB C4 O4 SING N N 20
CGB C4 C5 SING N N 21
CGB C4 H4 SING N N 22
CGB O4 HB SING N N 23
CGB C5 O5 SING N N 24
CGB C5 H5 SING N N 25
CGB O5 HC SING N N 26
#
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
CGB SMILES ACDLabs 10.04 OC12NC(CC1)C(O)C(O)C2O
CGB SMILES_CANONICAL CACTVS 3.341 O[C@@H]1[C@@H](O)[C@H](O)[C@]2(O)CC[C@H]1N2
CGB SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O)[C]2(O)CC[CH]1N2
CGB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@]2([C@H]([C@@H]([C@H]([C@@H]1N2)O)O)O)O
CGB SMILES "OpenEye OEToolkits" 1.5.0 C1CC2(C(C(C(C1N2)O)O)O)O
CGB InChI InChI 1.03 InChI=1S/C7H13NO4/c9-4-3-1-2-7(12,8-3)6(11)5(4)10/h3-6,8-12H,1-2H2/t3-,4+,5-,6+,7-/m1/s1
CGB InChIKey InChI 1.03 FXFBVZOJVHCEDO-IBISWUOJSA-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
CGB "SYSTEMATIC NAME" ACDLabs 10.04 (1R,2S,3R,4S,5R)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol
CGB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (1R,2S,3R,4S,5R)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CGB 'Create component' 2006-01-09 EBI
CGB 'Modify descriptor' 2011-06-04 RCSB
CGB 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CGB
_pdbx_chem_comp_synonyms.name (1S,2R,3S,4R,5S)-8-AZABICYCLO[3.2.1]OCTANE-1,2,3,4-TETROL
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id CGB
_pdbe_chem_comp_drugbank_details.drugbank_id DB04658
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Calystegine B2'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 127414-85-1
_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
CGB '(1S,2R,3S,4R,5S)-8-AZABICYCLO[3.2.1]OCTANE-1,2,3,4-TETROL' wwPDB ?
CGB 'Calystegine B(2)' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CGB
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04658
_pdbe_chem_comp_drugbank_classification.parent 'Tropane alkaloids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Tropane alkaloids'
_pdbe_chem_comp_drugbank_classification.superclass 'Alkaloids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as tropane alkaloids. These are organic compounds containing the nitrogenous bicyclic alkaloid parent N-Methyl-8-azabicyclo[3.2.1]octane.'
#
_pdbe_chem_comp_drugbank_targets.comp_id CGB
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04658
_pdbe_chem_comp_drugbank_targets.name 'Beta-glucosidase A'
_pdbe_chem_comp_drugbank_targets.organism 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)'
_pdbe_chem_comp_drugbank_targets.uniprot_id Q08638
_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
CGB O2 O 1.078 -2.542 1
CGB C2 C 0.803 -1.067 2
CGB N1 N 1.552 0.232 3
CGB C8 C 2.229 -0.517 4
CGB C7 C 2.228 0.983 5
CGB C6 C 0.801 1.531 6
CGB C3 C -0.697 -1.069 7
CGB O3 O -1.446 -2.369 8
CGB C4 C -1.448 0.230 9
CGB O4 O -2.948 0.229 10
CGB C5 C -0.700 1.530 11
CGB O5 O -1.451 2.828 12
#
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
CGB C2 O2 SINGLE BEGINDASH 1
CGB C2 N1 SINGLE NONE 2
CGB C2 C8 SINGLE NONE 3
CGB C2 C3 SINGLE NONE 4
CGB N1 C6 SINGLE NONE 5
CGB C8 C7 SINGLE NONE 6
CGB C7 C6 SINGLE NONE 7
CGB C6 C5 SINGLE NONE 8
CGB C3 O3 SINGLE BEGINWEDGE 9
CGB C3 C4 SINGLE NONE 10
CGB C4 O4 SINGLE BEGINDASH 11
CGB C4 C5 SINGLE NONE 12
CGB C5 O5 SINGLE BEGINWEDGE 13
#
_pdbe_chem_comp_substructure.comp_id CGB
_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 'C1CC2CC[C@H](C1)N2'
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C7H13N/c1-2-6-4-5-7(3-1)8-6/h6-8H,1-5H2/t6-,7?/m0/s1
_pdbe_chem_comp_substructure.substructure_inchikeys DGGKXQQCVPAUEA-PKPIPKONSA-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
CGB C2 S1 1
CGB N1 S1 1
CGB C8 S1 1
CGB C7 S1 1
CGB C6 S1 1
CGB C3 S1 1
CGB C4 S1 1
CGB C5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CGB
_pdbe_chem_comp_rdkit_properties.exactmw 175.084
_pdbe_chem_comp_rdkit_properties.amw 175.184
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 88.313
_pdbe_chem_comp_rdkit_properties.tpsa 92.950
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.477
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.128
_pdbe_chem_comp_rdkit_properties.chi0v 5.580
_pdbe_chem_comp_rdkit_properties.chi1v 3.014
_pdbe_chem_comp_rdkit_properties.chi2v 1.555
_pdbe_chem_comp_rdkit_properties.chi3v 1.555
_pdbe_chem_comp_rdkit_properties.chi4v 0.937
_pdbe_chem_comp_rdkit_properties.chi0n 18.580
_pdbe_chem_comp_rdkit_properties.chi1n 9.094
_pdbe_chem_comp_rdkit_properties.chi2n 1.555
_pdbe_chem_comp_rdkit_properties.chi3n 1.555
_pdbe_chem_comp_rdkit_properties.chi4n 0.937
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 2.068
_pdbe_chem_comp_rdkit_properties.kappa2 2.397
_pdbe_chem_comp_rdkit_properties.kappa3 0.915
_pdbe_chem_comp_rdkit_properties.Phi 0.413
#
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
CGB UniChem ChEMBL CHEMBL526330
CGB UniChem DrugBank DB04658
CGB UniChem PDBe CGB
CGB UniChem ZINC ZINC000012504453
CGB UniChem eMolecules 29257210
CGB UniChem 'PubChem TPHARMA' 16919355
CGB UniChem NMRShiftDB 60064348
CGB UniChem Nikkaji J657.463G
CGB UniChem BindingDb 36389
CGB UniChem 'Probes And Drugs' PD005924
CGB UniChem PubChem 124434
CGB UniChem SureChEMBL SCHEMBL2435745
CGB UniChem 'PubChem TPHARMA' 16081514
#
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
CGB O2 -2.590 0.597 -0.857 ETKDGv3 1
CGB C2 -1.327 0.133 -0.448 ETKDGv3 2
CGB N1 -0.628 -0.434 -1.598 ETKDGv3 3
CGB C8 -1.451 -1.049 0.533 ETKDGv3 4
CGB C7 -0.260 -1.944 0.186 ETKDGv3 5
CGB C6 0.437 -1.207 -0.965 ETKDGv3 6
CGB C3 -0.468 1.298 0.142 ETKDGv3 7
CGB O3 -1.117 1.860 1.254 ETKDGv3 8
CGB C4 0.952 0.800 0.551 ETKDGv3 9
CGB O4 1.831 1.883 0.722 ETKDGv3 10
CGB C5 1.538 -0.235 -0.456 ETKDGv3 11
CGB O5 2.574 -0.969 0.145 ETKDGv3 12
CGB HO -3.092 0.853 -0.040 ETKDGv3 13
CGB H1 -0.244 0.311 -2.227 ETKDGv3 14
CGB H8C1 -1.424 -0.726 1.596 ETKDGv3 15
CGB H8C2 -2.398 -1.604 0.353 ETKDGv3 16
CGB H7C1 -0.622 -2.934 -0.168 ETKDGv3 17
CGB H7C2 0.405 -2.101 1.063 ETKDGv3 18
CGB H6 0.870 -1.928 -1.692 ETKDGv3 19
CGB H3 -0.370 2.075 -0.653 ETKDGv3 20
CGB HA -0.691 2.741 1.420 ETKDGv3 21
CGB H4 0.861 0.296 1.538 ETKDGv3 22
CGB HB 1.919 2.340 -0.155 ETKDGv3 23
CGB H5 1.944 0.303 -1.345 ETKDGv3 24
CGB HC 3.353 -0.358 0.218 ETKDGv3 25
#