data_NGT
#
_chem_comp.id NGT
_chem_comp.name 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H13 N O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-01-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 219.258
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NGT
_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 1HP5
_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
NGT C1 C1 C 0 1 N N R N N N -5.806 65.559 9.960 0.628 1.085 0.411 C1 NGT 1
NGT C2 C2 C 0 1 N N R N N N -6.579 66.476 8.966 -0.793 0.805 0.882 C2 NGT 2
NGT C3 C3 C 0 1 N N R N N N -5.602 67.266 8.030 -1.592 -0.084 -0.057 C3 NGT 3
NGT C4 C4 C 0 1 N N S N N N -4.370 67.809 8.775 -1.147 0.073 -1.506 C4 NGT 4
NGT C5 C5 C 0 1 N N R N N N -3.663 66.668 9.538 0.374 -0.125 -1.547 C5 NGT 5
NGT C6 C6 C 0 1 N N N N N N -2.440 67.120 10.332 0.847 -0.215 -2.999 C6 NGT 6
NGT C7 C7 C 0 1 N N N N N N -7.038 64.431 8.057 0.284 -0.316 2.716 C7 NGT 7
NGT C8 C8 C 0 1 N N N N N N -7.695 63.335 7.251 0.438 -0.968 4.066 C8 NGT 8
NGT N2 N2 N 0 1 N N N N N N -7.439 65.624 8.155 -0.791 0.188 2.208 N2 NGT 9
NGT S1 S1 S 0 1 N N N N N N -5.587 64.002 8.967 1.552 -0.068 1.481 S1 NGT 10
NGT O3 O3 O 0 1 N N N N N N -6.301 68.324 7.392 -2.976 0.257 0.042 O3 NGT 11
NGT O4 O4 O 0 1 N N N N N N -3.483 68.394 7.838 -1.788 -0.909 -2.321 O4 NGT 12
NGT O5 O5 O 0 1 N N N N N N -4.603 66.034 10.488 0.973 0.994 -0.914 O5 NGT 13
NGT O6 O6 O 0 1 N N N N N N -1.740 65.997 10.869 2.263 -0.401 -3.028 O6 NGT 14
NGT HC1 HC1 H 0 1 N N N N N N -6.382 65.449 10.908 0.866 2.090 0.759 HC1 NGT 15
NGT HC2 HC2 H 0 1 N N N N N N -7.171 67.224 9.542 -1.313 1.759 0.961 HC2 NGT 16
NGT HC3 HC3 H 0 1 N N N N N N -5.221 66.548 7.266 -1.461 -1.124 0.242 HC3 NGT 17
NGT HC4 HC4 H 0 1 N N N N N N -4.691 68.579 9.514 -1.399 1.072 -1.864 HC4 NGT 18
NGT HC5 HC5 H 0 1 N N N N N N -3.319 65.955 8.752 0.641 -1.037 -1.014 HC5 NGT 19
NGT HC61 1HC6 H 0 0 N N N N N N -1.770 67.770 9.722 0.360 -1.060 -3.487 HC61 NGT 20
NGT HC62 2HC6 H 0 0 N N N N N N -2.711 67.854 11.125 0.590 0.704 -3.523 HC62 NGT 21
NGT HC81 1HC8 H 0 0 N N N N N N -7.340 62.281 7.164 1.470 -1.290 4.198 HC81 NGT 22
NGT HC82 2HC8 H 0 0 N N N N N N -8.754 63.283 7.595 0.178 -0.253 4.847 HC82 NGT 23
NGT HC83 3HC8 H 0 0 N N N N N N -7.786 63.722 6.209 -0.223 -1.832 4.129 HC83 NGT 24
NGT HO3 HO3 H 0 1 N N N N N N -5.708 68.803 6.824 -3.452 -0.324 -0.564 HO3 NGT 25
NGT HO4 HO4 H 0 1 N N N N N N -2.722 68.729 8.298 -1.476 -0.769 -3.226 HO4 NGT 26
NGT HO6 HO6 H 0 1 N N N N N N -0.978 66.278 11.363 2.519 -0.453 -3.959 HO6 NGT 27
#
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
NGT C1 C2 SING N N 1
NGT C1 S1 SING N N 2
NGT C1 O5 SING N N 3
NGT C1 HC1 SING N N 4
NGT C2 C3 SING N N 5
NGT C2 N2 SING N N 6
NGT C2 HC2 SING N N 7
NGT C3 C4 SING N N 8
NGT C3 O3 SING N N 9
NGT C3 HC3 SING N N 10
NGT C4 C5 SING N N 11
NGT C4 O4 SING N N 12
NGT C4 HC4 SING N N 13
NGT C5 C6 SING N N 14
NGT C5 O5 SING N N 15
NGT C5 HC5 SING N N 16
NGT C6 O6 SING N N 17
NGT C6 HC61 SING N N 18
NGT C6 HC62 SING N N 19
NGT C7 C8 SING N N 20
NGT C7 N2 DOUB N N 21
NGT C7 S1 SING N N 22
NGT C8 HC81 SING N N 23
NGT C8 HC82 SING N N 24
NGT C8 HC83 SING N N 25
NGT O3 HO3 SING N N 26
NGT O4 HO4 SING N N 27
NGT O6 HO6 SING N N 28
#
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
NGT SMILES ACDLabs 10.04 N1=C(SC2OC(C(O)C(O)C12)CO)C
NGT SMILES_CANONICAL CACTVS 3.341 CC1=N[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2S1
NGT SMILES CACTVS 3.341 CC1=N[CH]2[CH](O)[CH](O)[CH](CO)O[CH]2S1
NGT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=N[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2S1)CO)O)O
NGT SMILES "OpenEye OEToolkits" 1.5.0 CC1=NC2C(C(C(OC2S1)CO)O)O
NGT InChI InChI 1.03 InChI=1S/C8H13NO4S/c1-3-9-5-7(12)6(11)4(2-10)13-8(5)14-3/h4-8,10-12H,2H2,1H3/t4-,5-,6-,7-,8-/m1/s1
NGT InChIKey InChI 1.03 DRHXTSWSUAJOJZ-FMDGEEDCSA-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
NGT "SYSTEMATIC NAME" ACDLabs 10.04 (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
NGT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[5,6-d][1,3]thiazole-6,7-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NGT 'Create component' 2001-01-08 RCSB
NGT 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id NGT
_pdbe_chem_comp_drugbank_details.drugbank_id DB03747
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'N-Acetyl-glucosamine thiazoline'
_pdbe_chem_comp_drugbank_details.description
'N-Acetyl-glucosamine thiazoline (NAG-thiazoline) is an analog of the oxazolinium bicyclic intermediate leading from N-acetylglucosamine to 1,6-anhydro-N-acetylmuramic acid.'
_pdbe_chem_comp_drugbank_details.cas_number 179030-22-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id NGT
_pdbe_chem_comp_synonyms.name NAG-thiazoline
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id NGT
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03747
_pdbe_chem_comp_drugbank_classification.parent Monosaccharides
_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 monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.'
#
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
NGT DB03747 'Beta-hexosaminidase subunit beta' Humans P07686 unknown 1
NGT DB03747 B-N-acetylhexosaminidase 'Streptomyces plicatus' O85361 unknown 2
#
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
NGT C1 C 7.702 -0.750 1
NGT C2 C 7.702 0.750 2
NGT C3 C 6.404 1.500 3
NGT C4 C 5.104 0.750 4
NGT C5 C 5.104 -0.750 5
NGT C6 C 3.805 -1.500 6
NGT C7 C 9.997 0.000 7
NGT C8 C 11.497 0.000 8
NGT N2 N 9.122 1.207 9
NGT S1 S 9.122 -1.207 10
NGT O3 O 6.404 3.000 11
NGT O4 O 3.805 1.500 12
NGT O5 O 6.404 -1.500 13
NGT O6 O 3.805 -3.000 14
#
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
NGT C1 C2 SINGLE NONE 1
NGT C1 S1 SINGLE NONE 2
NGT C1 O5 SINGLE NONE 3
NGT C2 C3 SINGLE NONE 4
NGT C2 N2 SINGLE NONE 5
NGT C3 C4 SINGLE NONE 6
NGT C3 O3 SINGLE BEGINDASH 7
NGT C4 C5 SINGLE NONE 8
NGT C4 O4 SINGLE BEGINWEDGE 9
NGT C5 C6 SINGLE BEGINDASH 10
NGT C5 O5 SINGLE NONE 11
NGT C6 O6 SINGLE NONE 12
NGT C7 C8 SINGLE NONE 13
NGT C7 N2 DOUBLE NONE 14
NGT C7 S1 SINGLE NONE 15
#
_pdbe_chem_comp_substructure.comp_id NGT
_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 'C1=N[C@@H]2CCCO[C@@H]2S1'
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C6H9NOS/c1-2-5-6(8-3-1)9-4-7-5/h4-6H,1-3H2/t5-,6-/m1/s1
_pdbe_chem_comp_substructure.substructure_inchikeys BZUMLVGUHURTJN-PHDIDXHHSA-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
NGT C1 S1 1
NGT C2 S1 1
NGT C3 S1 1
NGT C4 S1 1
NGT C5 S1 1
NGT C7 S1 1
NGT N2 S1 1
NGT S1 S1 1
NGT O5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NGT
_pdbe_chem_comp_rdkit_properties.exactmw 219.057
_pdbe_chem_comp_rdkit_properties.amw 219.262
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 104.321
_pdbe_chem_comp_rdkit_properties.tpsa 82.280
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.041
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.248
_pdbe_chem_comp_rdkit_properties.chi0v 7.305
_pdbe_chem_comp_rdkit_properties.chi1v 4.193
_pdbe_chem_comp_rdkit_properties.chi2v 2.258
_pdbe_chem_comp_rdkit_properties.chi3v 2.258
_pdbe_chem_comp_rdkit_properties.chi4v 1.608
_pdbe_chem_comp_rdkit_properties.chi0n 19.488
_pdbe_chem_comp_rdkit_properties.chi1n 9.601
_pdbe_chem_comp_rdkit_properties.chi2n 1.511
_pdbe_chem_comp_rdkit_properties.chi3n 1.511
_pdbe_chem_comp_rdkit_properties.chi4n 0.936
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.953
_pdbe_chem_comp_rdkit_properties.kappa2 3.785
_pdbe_chem_comp_rdkit_properties.kappa3 1.569
_pdbe_chem_comp_rdkit_properties.Phi 0.798
#
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
NGT UniChem ChEMBL CHEMBL257158
NGT UniChem DrugBank DB03747
NGT UniChem PDBe NGT
NGT UniChem ZINC ZINC000016051892
NGT UniChem fdasrs ML5FHL557A
NGT UniChem SureChEMBL SCHEMBL1904292
NGT UniChem Nikkaji J760.469F
NGT UniChem BindingDb 50327038
NGT UniChem BRENDA 14895
NGT UniChem BRENDA 201151
NGT UniChem BRENDA 201153
NGT UniChem BRENDA 25011
NGT UniChem BRENDA 66270
NGT UniChem BRENDA 72742
NGT UniChem BRENDA 85284
NGT UniChem ChemicalBook CB42617756
NGT UniChem 'Probes And Drugs' PD059487
NGT UniChem 'PubChem TPHARMA' 14822642
NGT UniChem 'PubChem TPHARMA' 15863360
NGT UniChem PubChem 5289024
#
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
NGT C1 0.396 -0.935 -0.439 ETKDGv3 1
NGT C2 0.947 0.498 -0.594 ETKDGv3 2
NGT C3 -0.030 1.551 -0.032 ETKDGv3 3
NGT C4 -1.478 1.080 -0.254 ETKDGv3 4
NGT C5 -1.691 -0.289 0.457 ETKDGv3 5
NGT C6 -2.755 -1.143 -0.253 ETKDGv3 6
NGT C7 2.738 -0.575 0.374 ETKDGv3 7
NGT C8 4.010 -0.663 1.153 ETKDGv3 8
NGT N2 2.203 0.554 0.104 ETKDGv3 9
NGT S1 1.825 -2.022 -0.131 ETKDGv3 10
NGT O3 0.200 2.809 -0.616 ETKDGv3 11
NGT O4 -2.382 2.024 0.262 ETKDGv3 12
NGT O5 -0.491 -1.032 0.660 ETKDGv3 13
NGT O6 -3.008 -2.315 0.473 ETKDGv3 14
NGT HC1 -0.097 -1.273 -1.378 ETKDGv3 15
NGT HC2 1.134 0.682 -1.676 ETKDGv3 16
NGT HC3 0.132 1.650 1.065 ETKDGv3 17
NGT HC4 -1.647 0.955 -1.352 ETKDGv3 18
NGT HC5 -2.087 -0.070 1.474 ETKDGv3 19
NGT HC61 -3.701 -0.564 -0.320 ETKDGv3 20
NGT HC62 -2.443 -1.389 -1.293 ETKDGv3 21
NGT HC81 3.882 -0.166 2.137 ETKDGv3 22
NGT HC82 4.827 -0.163 0.592 ETKDGv3 23
NGT HC83 4.287 -1.725 1.320 ETKDGv3 24
NGT HO3 -0.013 2.738 -1.583 ETKDGv3 25
NGT HO4 -2.470 2.743 -0.417 ETKDGv3 26
NGT HO6 -2.289 -2.958 0.237 ETKDGv3 27
#