data_LXB
#
_chem_comp.id LXB
_chem_comp.name 2-acetamido-2-deoxy-beta-D-gulopyranose
_chem_comp.type 'D-saccharide, beta linking'
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C8 H15 N O6'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;N-acetyl-beta-D-gulosamine; 2-acetamido-2-deoxy-beta-D-gulose; 2-acetamido-2-deoxy-D-gulose;
2-acetamido-2-deoxy-gulose; 2-(acetylamino)-2-deoxy-beta-D-gulopyranose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-23
_chem_comp.pdbx_modified_date 2024-09-27
_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 LXB
_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 3D12
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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 LXB N-acetyl-beta-D-gulosamine PDB ?
2 LXB 2-acetamido-2-deoxy-beta-D-gulose PDB ?
3 LXB 2-acetamido-2-deoxy-D-gulose PDB ?
4 LXB 2-acetamido-2-deoxy-gulose PDB ?
5 LXB '2-(acetylamino)-2-deoxy-beta-D-gulopyranose' 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
LXB O1 O1 O 0 1 N Y N N N N 43.818 -59.203 -29.716 -0.891 -2.048 -0.244 O1 LXB 1
LXB C1 C1 C 0 1 N N R N N N 42.575 -59.751 -30.190 -0.136 -0.867 -0.520 C1 LXB 2
LXB C2 C2 C 0 1 N N R N N N 41.685 -59.516 -28.981 -0.774 0.327 0.196 C2 LXB 3
LXB C3 C3 C 0 1 N N S N N N 40.249 -60.062 -29.234 0.075 1.577 -0.056 C3 LXB 4
LXB C4 C4 C 0 1 N N R N N N 39.820 -60.273 -30.778 1.507 1.312 0.419 C4 LXB 5
LXB C5 C5 C 0 1 N N R N N N 40.900 -59.761 -31.880 2.057 0.080 -0.306 C5 LXB 6
LXB C6 C6 C 0 1 N N N N N N 40.252 -58.958 -33.078 3.466 -0.226 0.207 C6 LXB 7
LXB C7 C7 C 0 1 N N N N N N 42.462 -59.470 -26.469 -3.163 -0.153 0.189 C7 LXB 8
LXB C8 C8 C 0 1 N N N N N N 42.852 -60.296 -25.229 -4.555 0.068 -0.343 C8 LXB 9
LXB N2 N2 N 0 1 N N N N N N 42.266 -60.166 -27.778 -2.127 0.542 -0.322 N2 LXB 10
LXB O3 O3 O 0 1 N N N N N N 40.070 -61.315 -28.540 0.082 1.876 -1.453 O3 LXB 11
LXB O4 O4 O 0 1 N N N N N N 38.564 -59.541 -30.965 1.507 1.078 1.828 O4 LXB 12
LXB O5 O5 O 0 1 N N N N N N 42.073 -59.080 -31.346 1.204 -1.038 -0.055 O5 LXB 13
LXB O6 O6 O 0 1 N N N N N N 39.033 -58.284 -32.691 4.024 -1.303 -0.550 O6 LXB 14
LXB O7 O7 O 0 1 N N N N N N 42.498 -58.277 -26.389 -2.974 -0.956 1.078 O7 LXB 15
LXB HO1 HO1 H 0 1 N Y N N N N 44.411 -59.082 -30.448 -0.544 -2.845 -0.667 HO1 LXB 16
LXB H1 H1 H 0 1 N N N N N N 42.651 -60.798 -30.518 -0.127 -0.684 -1.595 H1 LXB 17
LXB H2 H2 H 0 1 N N N N N N 41.622 -58.431 -28.810 -0.821 0.127 1.266 H2 LXB 18
LXB H3 H3 H 0 1 N N N N N N 39.594 -59.266 -28.851 -0.343 2.419 0.495 H3 LXB 19
LXB H4 H4 H 0 1 N N N N N N 39.737 -61.356 -30.950 2.131 2.176 0.193 H4 LXB 20
LXB H5 H5 H 0 1 N N N N N N 41.286 -60.706 -32.290 2.095 0.276 -1.378 H5 LXB 21
LXB H61 H6 H 0 1 N N N N N N 40.974 -58.204 -33.424 4.093 0.658 0.097 H61 LXB 22
LXB H62 H6A H 0 1 N N N N N N 40.003 -59.678 -33.872 3.416 -0.509 1.258 H62 LXB 23
LXB H81 H8 H 0 1 N N N N N N 42.945 -61.356 -25.508 -5.254 -0.577 0.188 H81 LXB 24
LXB H82 H8A H 0 1 N N N N N N 43.814 -59.935 -24.836 -4.839 1.110 -0.197 H82 LXB 25
LXB H83 H8B H 0 1 N N N N N N 42.076 -60.187 -24.457 -4.579 -0.168 -1.407 H83 LXB 26
LXB HN2 HN2 H 0 1 N N N N N N 42.542 -61.125 -27.848 -2.278 1.184 -1.033 HN2 LXB 27
LXB HO3 HO3 H 0 1 N Y N N N N 40.031 -62.024 -29.171 0.602 2.658 -1.685 HO3 LXB 28
LXB HO4 HO4 H 0 1 N Y N N N N 38.160 -59.383 -30.120 2.384 0.902 2.198 HO4 LXB 29
LXB HO6 HO6 H 0 1 N Y N N N N 39.037 -58.136 -31.753 4.918 -1.551 -0.279 HO6 LXB 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
LXB C1 O1 SING N N 1
LXB O1 HO1 SING N N 2
LXB O5 C1 SING N N 3
LXB C1 C2 SING N N 4
LXB C1 H1 SING N N 5
LXB C3 C2 SING N N 6
LXB C2 N2 SING N N 7
LXB C2 H2 SING N N 8
LXB C4 C3 SING N N 9
LXB C3 O3 SING N N 10
LXB C3 H3 SING N N 11
LXB C5 C4 SING N N 12
LXB O4 C4 SING N N 13
LXB C4 H4 SING N N 14
LXB C6 C5 SING N N 15
LXB C5 O5 SING N N 16
LXB C5 H5 SING N N 17
LXB C6 O6 SING N N 18
LXB C6 H61 SING N N 19
LXB C6 H62 SING N N 20
LXB N2 C7 SING N N 21
LXB C7 O7 DOUB N N 22
LXB C7 C8 SING N N 23
LXB C8 H81 SING N N 24
LXB C8 H82 SING N N 25
LXB C8 H83 SING N N 26
LXB N2 HN2 SING N N 27
LXB O3 HO3 SING N N 28
LXB O4 HO4 SING N N 29
LXB 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
LXB SMILES ACDLabs 10.04 'O=C(NC1C(O)C(O)C(OC1O)CO)C'
LXB SMILES_CANONICAL CACTVS 3.341 'CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@H]1O'
LXB SMILES CACTVS 3.341 'CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O'
LXB SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CC(=O)N[C@@H]1[C@@H]([C@H]([C@H](O[C@H]1O)CO)O)O'
LXB SMILES 'OpenEye OEToolkits' 1.5.0 'CC(=O)NC1C(C(C(OC1O)CO)O)O'
LXB InChI InChI 1.03 'InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7+,8-/m1/s1'
LXB InChIKey InChI 1.03 OVRNDRQMDRJTHS-QQGCVABSSA-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
LXB 'SYSTEMATIC NAME' ACDLabs 10.04 '2-(acetylamino)-2-deoxy-beta-D-gulopyranose'
LXB 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 'N-[(2R,3R,4S,5R,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanamide'
LXB 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGulpNAcb
LXB 'COMMON NAME' GMML 1.0 N-acetyl-b-D-gulopyranosamine
LXB 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GulpNAc
LXB 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GulNAc
#
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
LXB 'CARBOHYDRATE ISOMER' D PDB ?
LXB 'CARBOHYDRATE RING' pyranose PDB ?
LXB 'CARBOHYDRATE ANOMER' beta PDB ?
LXB '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
LXB 'Create component' 2008-07-23 RCSB
LXB 'Modify descriptor' 2011-06-04 RCSB
LXB 'Other modification' 2019-08-12 RCSB
LXB 'Other modification' 2019-12-19 RCSB
LXB 'Other modification' 2020-07-03 RCSB
LXB 'Modify name' 2020-07-17 RCSB
LXB 'Modify synonyms' 2020-07-17 RCSB
LXB 'Modify atom id' 2020-07-17 RCSB
LXB 'Modify component atom id' 2020-07-17 RCSB
LXB 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id LXB
_pdbx_chem_comp_pcm.modified_residue_id ASN
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Carbohydrate
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C1
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ND2
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
LXB N-acetyl-beta-D-gulosamine wwPDB ?
LXB 2-acetamido-2-deoxy-beta-D-gulose wwPDB ?
LXB 2-acetamido-2-deoxy-D-gulose wwPDB ?
LXB 2-acetamido-2-deoxy-gulose wwPDB ?
LXB 2-(acetylamino)-2-deoxy-beta-D-gulopyranose wwPDB ?
#
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
LXB O1 O 9.002 1.500 1
LXB C1 C 7.702 0.750 2
LXB C2 C 7.702 -0.750 3
LXB C3 C 6.404 -1.500 4
LXB C4 C 5.104 -0.750 5
LXB C5 C 5.104 0.750 6
LXB C6 C 3.805 1.500 7
LXB C7 C 10.301 -0.750 8
LXB C8 C 11.600 -1.500 9
LXB N2 N 9.002 -1.500 10
LXB O3 O 6.404 -3.000 11
LXB O4 O 3.805 -1.500 12
LXB O5 O 6.404 1.500 13
LXB O6 O 3.805 3.000 14
LXB O7 O 10.301 0.750 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
LXB C1 O1 SINGLE BEGINWEDGE 1
LXB O5 C1 SINGLE NONE 2
LXB C1 C2 SINGLE NONE 3
LXB C3 C2 SINGLE NONE 4
LXB C2 N2 SINGLE BEGINDASH 5
LXB C4 C3 SINGLE NONE 6
LXB C3 O3 SINGLE BEGINDASH 7
LXB C5 C4 SINGLE NONE 8
LXB C4 O4 SINGLE BEGINWEDGE 9
LXB C5 C6 SINGLE BEGINWEDGE 10
LXB C5 O5 SINGLE NONE 11
LXB C6 O6 SINGLE NONE 12
LXB N2 C7 SINGLE NONE 13
LXB C7 O7 DOUBLE NONE 14
LXB C7 C8 SINGLE 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
LXB MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
LXB amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
LXB pyranose F2 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
LXB C1 S1 1
LXB C2 S1 1
LXB C3 S1 1
LXB C4 S1 1
LXB C5 S1 1
LXB O5 S1 1
LXB N2 F1 1
LXB C7 F1 1
LXB O7 F1 1
LXB C8 F1 1
LXB C4 F2 1
LXB C5 F2 1
LXB O5 F2 1
LXB C1 F2 1
LXB C2 F2 1
LXB C3 F2 1
LXB O1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LXB
_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 1.322
_pdbe_chem_comp_rdkit_properties.chi3v 1.322
_pdbe_chem_comp_rdkit_properties.chi4v 0.756
_pdbe_chem_comp_rdkit_properties.chi0n 21.897
_pdbe_chem_comp_rdkit_properties.chi1n 10.456
_pdbe_chem_comp_rdkit_properties.chi2n 1.322
_pdbe_chem_comp_rdkit_properties.chi3n 1.322
_pdbe_chem_comp_rdkit_properties.chi4n 0.756
_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
LXB UniChem ZINC ZINC000000901459
LXB UniChem PubChem 11861121
#
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
LXB O1 -0.721 -2.711 0.703 ETKDGv3 1
LXB C1 -0.177 -1.450 0.999 ETKDGv3 2
LXB C2 0.824 -1.025 -0.109 ETKDGv3 3
LXB C3 0.079 -0.766 -1.450 ETKDGv3 4
LXB C4 -1.396 -0.339 -1.238 ETKDGv3 5
LXB C5 -1.557 0.331 0.147 ETKDGv3 6
LXB C6 -2.985 0.863 0.338 ETKDGv3 7
LXB C7 2.911 0.437 -0.174 ETKDGv3 8
LXB C8 3.661 1.621 0.342 ETKDGv3 9
LXB N2 1.601 0.143 0.335 ETKDGv3 10
LXB O3 0.766 0.158 -2.260 ETKDGv3 11
LXB O4 -2.230 -1.469 -1.331 ETKDGv3 12
LXB O5 -1.243 -0.534 1.234 ETKDGv3 13
LXB O6 -3.086 1.572 1.544 ETKDGv3 14
LXB O7 3.445 -0.311 -1.037 ETKDGv3 15
LXB HO1 -0.009 -3.383 0.870 ETKDGv3 16
LXB H1 0.393 -1.530 1.953 ETKDGv3 17
LXB H2 1.532 -1.872 -0.257 ETKDGv3 18
LXB H3 0.071 -1.727 -2.011 ETKDGv3 19
LXB H4 -1.670 0.394 -2.035 ETKDGv3 20
LXB H5 -0.884 1.215 0.186 ETKDGv3 21
LXB H61 -3.701 0.014 0.373 ETKDGv3 22
LXB H62 -3.275 1.518 -0.515 ETKDGv3 23
LXB H81 3.010 2.520 0.306 ETKDGv3 24
LXB H82 3.969 1.435 1.392 ETKDGv3 25
LXB H83 4.566 1.809 -0.274 ETKDGv3 26
LXB HN2 1.241 0.735 1.117 ETKDGv3 27
LXB HO3 0.630 1.063 -1.875 ETKDGv3 28
LXB HO4 -3.099 -1.166 -1.705 ETKDGv3 29
LXB HO6 -2.665 2.457 1.390 ETKDGv3 30
#