data_GCS
#
_chem_comp.id GCS
_chem_comp.name 2-amino-2-deoxy-beta-D-glucopyranose
_chem_comp.type 'D-saccharide, beta linking'
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C6 H13 N O5'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
'beta-D-glucosamine; 2-amino-2-deoxy-beta-D-glucose; 2-amino-2-deoxy-D-glucose; 2-amino-2-deoxy-glucose; D-GLUCOSAMINE'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-06-20
_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 179.171
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GCS
_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 1QGI
_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 GCS beta-D-glucosamine PDB ?
2 GCS 2-amino-2-deoxy-beta-D-glucose PDB ?
3 GCS 2-amino-2-deoxy-D-glucose PDB ?
4 GCS 2-amino-2-deoxy-glucose PDB ?
5 GCS D-GLUCOSAMINE 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
GCS C1 C1 C 0 1 N N R N N N 20.309 45.844 45.851 1.385 -0.247 0.637 C1 GCS 1
GCS C2 C2 C 0 1 N N R N N N 21.106 44.545 45.841 0.298 0.219 1.607 C2 GCS 2
GCS C3 C3 C 0 1 N N R N N N 21.407 44.209 44.416 -1.069 -0.233 1.085 C3 GCS 3
GCS C4 C4 C 0 1 N N S N N N 20.111 44.050 43.598 -1.228 0.254 -0.359 C4 GCS 4
GCS C5 C5 C 0 1 N N R N N N 19.538 45.466 43.471 -0.026 -0.215 -1.181 C5 GCS 5
GCS C6 C6 C 0 1 N N N N N N 18.173 45.544 42.622 -0.193 0.240 -2.632 C6 GCS 6
GCS N2 N2 N 0 1 N N N N N N 22.354 44.690 46.630 0.537 -0.367 2.933 N2 GCS 7
GCS O1 O1 O 0 1 N Y N N N N 19.650 46.418 47.033 2.666 0.146 1.132 O1 GCS 8
GCS O3 O3 O 0 1 N N N N N N 22.221 42.928 44.354 -2.107 0.321 1.895 O3 GCS 9
GCS O4 O4 O 0 1 N N N N N N 20.904 43.963 42.404 -2.429 -0.283 -0.918 O4 GCS 10
GCS O5 O5 O 0 1 N N N N N N 19.211 45.844 44.868 1.172 0.340 -0.645 O5 GCS 11
GCS O6 O6 O 0 1 N N N N N N 17.624 46.975 42.524 0.924 -0.202 -3.403 O6 GCS 12
GCS H1 H1 H 0 1 N N N N N N 21.215 46.468 45.674 1.349 -1.333 0.548 H1 GCS 13
GCS H2 H2 H 0 1 N N N N N N 20.517 43.723 46.311 0.318 1.306 1.681 H2 GCS 14
GCS H3 H31 H 0 1 N N N N N N 21.994 45.046 43.973 -1.127 -1.321 1.112 H3 GCS 15
GCS H4 H4 H 0 1 N N N N N N 19.330 43.310 43.891 -1.275 1.343 -0.372 H4 GCS 16
GCS H5 H5 H 0 1 N N N N N N 20.271 46.121 42.946 0.032 -1.303 -1.148 H5 GCS 17
GCS H61 H61 H 0 1 N N N N N N 18.303 45.093 41.610 -1.109 -0.183 -3.043 H61 GCS 18
GCS H62 H62 H 0 1 N N N N N N 17.405 44.846 43.031 -0.250 1.328 -2.666 H62 GCS 19
GCS HN21 HN21 H 0 0 N N N N N N 22.887 43.820 46.623 1.445 -0.045 3.233 HN21 GCS 20
GCS HN22 HN22 H 0 0 N Y N N N N 22.165 45.010 47.579 -0.138 0.044 3.558 HN22 GCS 21
GCS HO1 HO1 H 0 1 N Y N N N N 19.153 47.227 47.039 3.321 -0.166 0.493 HO1 GCS 22
GCS HO3 H32 H 0 1 N Y N N N N 22.412 42.714 43.448 -1.969 -0.010 2.793 HO3 GCS 23
GCS HO4 HO4 H 0 1 N Y N N N N 20.104 43.865 41.899 -2.485 0.044 -1.826 HO4 GCS 24
GCS HO6 HO6 H 0 1 N Y N N N N 16.818 47.021 42.022 0.779 0.105 -4.308 HO6 GCS 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
GCS C1 C2 SING N N 1
GCS C1 O1 SING N N 2
GCS C1 O5 SING N N 3
GCS C1 H1 SING N N 4
GCS C2 C3 SING N N 5
GCS C2 N2 SING N N 6
GCS C2 H2 SING N N 7
GCS C3 C4 SING N N 8
GCS C3 O3 SING N N 9
GCS C3 H3 SING N N 10
GCS C4 C5 SING N N 11
GCS C4 O4 SING N N 12
GCS C4 H4 SING N N 13
GCS C5 C6 SING N N 14
GCS C5 O5 SING N N 15
GCS C5 H5 SING N N 16
GCS C6 O6 SING N N 17
GCS C6 H61 SING N N 18
GCS C6 H62 SING N N 19
GCS N2 HN21 SING N N 20
GCS N2 HN22 SING N N 21
GCS O1 HO1 SING N N 22
GCS O3 HO3 SING N N 23
GCS O4 HO4 SING N N 24
GCS O6 HO6 SING N N 25
#
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
GCS SMILES ACDLabs 10.04 'OC1C(O)C(OC(O)C1N)CO'
GCS SMILES_CANONICAL CACTVS 3.341 'N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O'
GCS SMILES CACTVS 3.341 'N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O'
GCS SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)N)O)O)O'
GCS SMILES 'OpenEye OEToolkits' 1.5.0 'C(C1C(C(C(C(O1)O)N)O)O)O'
GCS InChI InChI 1.03 'InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6-/m1/s1'
GCS InChIKey InChI 1.03 MSWZFWKMSRAUBD-QZABAPFNSA-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
GCS 'SYSTEMATIC NAME' ACDLabs 10.04 2-amino-2-deoxy-beta-D-glucopyranose
GCS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R,3R,4R,5S,6R)-3-amino-6-(hydroxymethyl)oxane-2,4,5-triol'
GCS 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNb
GCS 'COMMON NAME' GMML 1.0 b-D-glucopyranosamine
GCS 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpN
GCS 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcN
#
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
GCS 'CARBOHYDRATE ISOMER' D PDB ?
GCS 'CARBOHYDRATE RING' pyranose PDB ?
GCS 'CARBOHYDRATE ANOMER' beta PDB ?
GCS '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
GCS 'Create component' 2000-06-20 RCSB
GCS 'Modify descriptor' 2011-06-04 RCSB
GCS 'Other modification' 2019-08-12 RCSB
GCS 'Other modification' 2019-12-19 RCSB
GCS 'Other modification' 2020-07-03 RCSB
GCS 'Modify name' 2020-07-17 RCSB
GCS 'Modify synonyms' 2020-07-17 RCSB
GCS 'Modify atom id' 2020-07-17 RCSB
GCS 'Modify component atom id' 2020-07-17 RCSB
GCS 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id GCS
_pdbx_chem_comp_pcm.modified_residue_id GHP
_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 O4
_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
GCS beta-D-glucosamine wwPDB ?
GCS 2-amino-2-deoxy-beta-D-glucose wwPDB ?
GCS 2-amino-2-deoxy-D-glucose wwPDB ?
GCS 2-amino-2-deoxy-glucose wwPDB ?
GCS D-GLUCOSAMINE wwPDB ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
GCS C1 C 7.702 0.750 1
GCS C2 C 7.702 -0.750 2
GCS C3 C 6.404 -1.500 3
GCS C4 C 5.104 -0.750 4
GCS C5 C 5.104 0.750 5
GCS C6 C 3.805 1.500 6
GCS N2 N 9.002 -1.500 7
GCS O1 O 9.002 1.500 8
GCS O3 O 6.404 -3.000 9
GCS O4 O 3.805 -1.500 10
GCS O5 O 6.404 1.500 11
GCS O6 O 3.805 3.000 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
GCS C1 C2 SINGLE NONE 1
GCS C1 O1 SINGLE BEGINWEDGE 2
GCS C1 O5 SINGLE NONE 3
GCS C2 C3 SINGLE NONE 4
GCS C2 N2 SINGLE BEGINDASH 5
GCS C3 C4 SINGLE NONE 6
GCS C3 O3 SINGLE BEGINWEDGE 7
GCS C4 C5 SINGLE NONE 8
GCS C4 O4 SINGLE BEGINDASH 9
GCS C5 C6 SINGLE BEGINWEDGE 10
GCS C5 O5 SINGLE NONE 11
GCS C6 O6 SINGLE NONE 12
#
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
GCS MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
GCS 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
GCS C1 S1 1
GCS C2 S1 1
GCS C3 S1 1
GCS C4 S1 1
GCS C5 S1 1
GCS O5 S1 1
GCS C4 F1 1
GCS C5 F1 1
GCS O5 F1 1
GCS C1 F1 1
GCS C2 F1 1
GCS C3 F1 1
GCS O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GCS
_pdbe_chem_comp_rdkit_properties.exactmw 179.079
_pdbe_chem_comp_rdkit_properties.amw 179.172
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 87.916
_pdbe_chem_comp_rdkit_properties.tpsa 116.170
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.255
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.955
_pdbe_chem_comp_rdkit_properties.chi0v 5.488
_pdbe_chem_comp_rdkit_properties.chi1v 2.698
_pdbe_chem_comp_rdkit_properties.chi2v 1.108
_pdbe_chem_comp_rdkit_properties.chi3v 1.108
_pdbe_chem_comp_rdkit_properties.chi4v 0.558
_pdbe_chem_comp_rdkit_properties.chi0n 18.488
_pdbe_chem_comp_rdkit_properties.chi1n 8.726
_pdbe_chem_comp_rdkit_properties.chi2n 1.108
_pdbe_chem_comp_rdkit_properties.chi3n 1.108
_pdbe_chem_comp_rdkit_properties.chi4n 0.558
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.221
_pdbe_chem_comp_rdkit_properties.kappa2 3.649
_pdbe_chem_comp_rdkit_properties.kappa3 1.582
_pdbe_chem_comp_rdkit_properties.Phi 0.675
#
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
GCS UniChem ChEMBL CHEMBL234432
GCS UniChem 'Guide to Pharmacology' 4535
GCS UniChem 'KEGG LIGAND' C08349
GCS UniChem ChEBI 28393
GCS UniChem ZINC ZINC000003860468
GCS UniChem fdasrs 58L064K8RR
GCS UniChem HMDB HMDB0030091
GCS UniChem 'PubChem TPHARMA' 15017247
GCS UniChem NMRShiftDB 20213218
GCS UniChem ACTor 14257-69-3
GCS UniChem ACTor 90-77-7
GCS UniChem ACTor 9012-76-4
GCS UniChem Nikkaji J419.923E
GCS UniChem 'EPA CompTox Dashboard' DTXSID4023098
GCS UniChem MetaboLights MTBLC28393
GCS UniChem BRENDA 11229
GCS UniChem BRENDA 158195
GCS UniChem 'Probes And Drugs' PD014488
GCS UniChem ACTor 28905-10-4
GCS UniChem eMolecules 551292
GCS UniChem SureChEMBL SCHEMBL3263
GCS UniChem PubChem 441477
#
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
GCS C1 -0.662 -1.516 0.146 ETKDGv3 1
GCS C2 -1.709 -0.378 0.005 ETKDGv3 2
GCS C3 -1.049 0.962 -0.418 ETKDGv3 3
GCS C4 0.417 1.012 0.041 ETKDGv3 4
GCS C5 1.185 -0.188 -0.584 ETKDGv3 5
GCS C6 2.466 -0.528 0.194 ETKDGv3 6
GCS N2 -2.750 -0.768 -0.950 ETKDGv3 7
GCS O1 -0.163 -1.587 1.460 ETKDGv3 8
GCS O3 -1.778 2.057 0.079 ETKDGv3 9
GCS O4 1.011 2.216 -0.376 ETKDGv3 10
GCS O5 0.401 -1.365 -0.781 ETKDGv3 11
GCS O6 3.361 0.549 0.142 ETKDGv3 12
GCS H1 -1.158 -2.487 -0.086 ETKDGv3 13
GCS H2 -2.198 -0.245 0.996 ETKDGv3 14
GCS H3 -1.048 1.038 -1.529 ETKDGv3 15
GCS H4 0.454 0.938 1.154 ETKDGv3 16
GCS H5 1.507 0.129 -1.601 ETKDGv3 17
GCS H61 2.941 -1.423 -0.266 ETKDGv3 18
GCS H62 2.226 -0.764 1.254 ETKDGv3 19
GCS HN21 -2.325 -0.888 -1.899 ETKDGv3 20
GCS HN22 -3.455 0.002 -1.014 ETKDGv3 21
GCS HO1 -0.878 -1.987 2.021 ETKDGv3 22
GCS HO3 -1.710 2.041 1.069 ETKDGv3 23
GCS HO4 0.752 2.911 0.284 ETKDGv3 24
GCS HO6 4.161 0.267 0.657 ETKDGv3 25
#